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This page was generated on 2025-08-09 12:04 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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 205/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.15.1  (landing page)
Pierrick Roger
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

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: 2025-08-08 20:28:36 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 20:29:55 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 79.2 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 24.04.2 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 [2025-08-08 20:29:31.226][biodb::testContext]
biodb.INFO [2025-08-08 20:29:31.229][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-08 20:29:31.230][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-08-08 20:29:31.231][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-08 20:29:31.232][biodb::testContext]
biodb.INFO [2025-08-08 20:29:31.239][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-08-08 20:29:31.241][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-08-08 20:29:31.248][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-08 20:29:31.249][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-08 20:29:31.250][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-08 20:29:31.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.255][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-08 20:29:31.275][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-08 20:29:31.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.279][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.DEBUG[2025-08-08 20:29:31.280][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-08 20:29:31.281][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-08 20:29:31.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.285][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-08 20:29:31.286][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-08 20:29:31.287][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-08 20:29:31.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.291][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-08 20:29:31.292][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-08 20:29:31.293][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-08 20:29:31.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.297][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-08 20:29:31.298][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-08 20:29:31.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.311][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-08 20:29:31.312][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-08 20:29:31.313][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-08 20:29:31.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.317][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-08 20:29:31.318][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-08 20:29:31.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.320][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.DEBUG[2025-08-08 20:29:31.321][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-08 20:29:31.322][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-08 20:29:31.323][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-08 20:29:31.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.326][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-08 20:29:31.327][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-08 20:29:31.328][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-08 20:29:31.329][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-08 20:29:31.330][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-08 20:29:31.331][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-08 20:29:31.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.335][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-08 20:29:31.336][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-08 20:29:31.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.339][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-08 20:29:31.340][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-08 20:29:31.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.342][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.DEBUG[2025-08-08 20:29:31.343][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-08 20:29:31.344][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-08 20:29:31.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.348][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-08 20:29:31.349][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-08 20:29:31.350][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-08 20:29:31.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.353][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-08 20:29:31.354][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-08 20:29:31.358][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-08 20:29:31.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.362][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-08 20:29:31.363][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-08 20:29:31.364][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-08 20:29:31.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.370][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-08 20:29:31.401][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:31.417][self$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[2025-08-08 20:29:31.418][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:31.420][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-08 20:29:31.421][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:31.422][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-08 20:29:31.424][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:31.425][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-08 20:29:31.427][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-08 20:29:31.428][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-08 20:29:31.430][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:31.431][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-08 20:29:31.432][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-08 20:29:31.434][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:31.435][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:31.436][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-08 20:29:31.436][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-08 20:29:31.436][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-08 20:29:31.436][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-08 20:29:31.436][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-08 20:29:31.438][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-08 20:29:31.439][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:31.440][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:31.441][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-08 20:29:31.442][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:31.443][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:31.443][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-08 20:29:31.444][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:31.445][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-08 20:29:31.446][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-08 20:29:31.447][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:31.448][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:31.449][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-08 20:29:31.451][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:31.452][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-08 20:29:31.453][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:31.454][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-08 20:29:31.455][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:31.456][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-08 20:29:31.456][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:31.457][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-08 20:29:31.458][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-08 20:29:31.459][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-08 20:29:31.460][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:31.461][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-08 20:29:31.462][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-08 20:29:31.463][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:31.464][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:31.465][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-08 20:29:31.465][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-08 20:29:31.465][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-08 20:29:31.465][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-08 20:29:31.465][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-08 20:29:31.466][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-08 20:29:31.467][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:31.468][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:31.469][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-08 20:29:31.470][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:31.470][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:31.471][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-08 20:29:31.472][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:31.473][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-08 20:29:31.474][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-08 20:29:31.475][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:31.476][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:31.477][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-08 20:29:31.479][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:31.480][self$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[2025-08-08 20:29:31.481][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:31.481][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-08 20:29:31.482][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:31.483][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-08 20:29:31.484][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:31.485][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-08 20:29:31.486][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-08 20:29:31.487][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-08 20:29:31.488][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:31.489][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-08 20:29:31.490][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-08 20:29:31.491][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:31.492][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:31.493][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:31.494][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-08 20:29:31.495][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:31.496][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:31.496][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-08 20:29:31.497][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:31.498][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:31.499][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-08 20:29:31.500][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:31.501][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-08 20:29:31.502][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-08 20:29:31.503][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:31.504][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:31.505][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-08 20:29:31.506][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:31.507][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-08 20:29:31.508][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:31.509][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-08 20:29:31.510][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:31.511][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-08 20:29:31.512][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:31.513][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-08 20:29:31.514][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-08 20:29:31.515][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-08 20:29:31.516][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:31.517][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-08 20:29:31.518][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-08 20:29:31.518][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:31.524][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:31.525][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:31.526][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-08 20:29:31.527][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:31.527][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:31.528][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-08 20:29:31.529][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:31.530][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:31.531][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-08 20:29:31.532][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:31.533][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-08 20:29:31.534][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-08 20:29:31.534][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:31.535][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:31.539][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-08 20:29:31.540][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.549][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[2025-08-08 20:29:31.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.557][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".
biodb.DEBUG[2025-08-08 20:29:31.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.561][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[2025-08-08 20:29:31.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.574][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.DEBUG[2025-08-08 20:29:31.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.578][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[2025-08-08 20:29:31.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.590][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[2025-08-08 20:29:31.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.608][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-08 20:29:31.613][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-08 20:29:31.614][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-08 20:29:31.615][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-08 20:29:31.617][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-08 20:29:31.618][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-08 20:29:31.619][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-08 20:29:31.621][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-08 20:29:31.622][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-08 20:29:31.623][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-08 20:29:31.625][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-08 20:29:31.626][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-08 20:29:31.627][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-08 20:29:31.629][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-08 20:29:31.630][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-08 20:29:31.631][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-08 20:29:31.633][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-08 20:29:31.635][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-08 20:29:31.637][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-08 20:29:31.639][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-08 20:29:31.641][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-08 20:29:31.643][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-08 20:29:31.645][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-08 20:29:31.647][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-08 20:29:31.649][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-08 20:29:31.651][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-08 20:29:31.653][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-08 20:29:31.654][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-08 20:29:31.655][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-08 20:29:31.657][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-08 20:29:31.658][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-08 20:29:31.659][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-08 20:29:31.660][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-08 20:29:31.662][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-08 20:29:31.663][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-08 20:29:31.664][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-08 20:29:31.666][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-08 20:29:31.667][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-08 20:29:31.668][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-08 20:29:31.670][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-08 20:29:31.671][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-08 20:29:31.672][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-08 20:29:31.673][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-08 20:29:31.675][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-08 20:29:31.676][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-08 20:29:31.677][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-08 20:29:31.679][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-08 20:29:31.680][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-08 20:29:31.681][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-08 20:29:31.683][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-08 20:29:31.684][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-08 20:29:31.685][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-08 20:29:31.686][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-08 20:29:31.688][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-08 20:29:31.689][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-08 20:29:31.697][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-08 20:29:31.700][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-08 20:29:31.701][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-08 20:29:31.703][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-08 20:29:31.704][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-08 20:29:31.706][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-08 20:29:31.708][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-08 20:29:31.709][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-08 20:29:31.711][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-08 20:29:31.712][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-08 20:29:31.714][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-08 20:29:31.715][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-08 20:29:31.717][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-08 20:29:31.718][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-08 20:29:31.720][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-08 20:29:31.721][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-08 20:29:31.723][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-08 20:29:31.724][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-08 20:29:31.726][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-08 20:29:31.727][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-08 20:29:31.729][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-08 20:29:31.730][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-08 20:29:31.732][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-08 20:29:31.733][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-08 20:29:31.735][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-08 20:29:31.736][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-08 20:29:31.738][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-08 20:29:31.739][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-08 20:29:31.761][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-08 20:29:31.763][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-08-08 20:29:31.766][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-08 20:29:31.767][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.769][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:31.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:31.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:31.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:31.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:31.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:31.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:31.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:31.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:31.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:31.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.806][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[2025-08-08 20:29:31.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:31.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:31.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:31.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:31.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:31.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:31.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:31.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:31.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.832][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[2025-08-08 20:29:31.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:31.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:31.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:31.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:31.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.845][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[2025-08-08 20:29:31.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:31.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:31.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:31.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:31.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.858][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[2025-08-08 20:29:31.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:31.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:31.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:31.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:31.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:31.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:31.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:31.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:31.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:31.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:31.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:31.879][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-08 20:29:31.889][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-08 20:29:31.891][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:31.892][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-08 20:29:31.893][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:31.894][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-08 20:29:31.895][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:31.896][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-08 20:29:31.897][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:31.898][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-08 20:29:31.899][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-08 20:29:31.900][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-08 20:29:31.901][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:31.902][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-08 20:29:31.903][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-08 20:29:31.904][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-08 20:29:31.904][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-08 20:29:31.904][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-08 20:29:31.904][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-08 20:29:31.904][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-08 20:29:31.904][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-08 20:29:31.904][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-08 20:29:31.904][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-08 20:29:31.904][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-08 20:29:31.904][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-08 20:29:31.904][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-08 20:29:31.905][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:31.906][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-08 20:29:31.906][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-08 20:29:31.906][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-08 20:29:31.907][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-08 20:29:31.908][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:31.909][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:31.910][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-08 20:29:31.911][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:31.912][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:31.913][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-08 20:29:31.914][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-08 20:29:31.914][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-08 20:29:31.915][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-08 20:29:31.915][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-08 20:29:31.916][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:31.917][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-08 20:29:31.917][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-08 20:29:31.924][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-08 20:29:31.925][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-08 20:29:31.927][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-08 20:29:31.928][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-08 20:29:31.930][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-08 20:29:31.931][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-08 20:29:31.953][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-08 20:29:31.969][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-08 20:29:31.978][biodb::testThat]
biodb.INFO [2025-08-08 20:29:31.979][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-08-08 20:29:31.980][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-08 20:29:31.981][biodb::testThat]
biodb.TRACE[2025-08-08 20:29:31.991][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-08-08 20:29:31.993][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:31.996][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:32.004][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:32.005][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:32.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:32.017][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:32.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:32.019][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:32.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:32.029][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.030][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.031][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.031][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.048][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:32.049][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:32.050][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.051][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.077][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:32.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:32.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.081][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:32.082][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:32.083][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.084][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.085][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:32.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:32.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.089][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:32.090][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:32.091][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.092][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.093][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:32.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:32.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.098][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:32.099][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:32.099][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.100][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.102][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:32.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:32.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.106][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:32.107][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:32.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.108][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.110][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:32.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:32.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.114][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:32.115][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:32.116][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.117][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.118][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:32.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:32.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.122][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:32.123][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:32.124][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.125][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:32.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:32.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.130][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:32.131][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:32.132][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.133][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.134][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:32.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:32.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.138][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:32.139][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:32.140][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.141][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.142][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:32.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:32.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.146][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:32.147][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:32.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.149][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.150][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:32.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:32.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.158][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.166][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:32.230][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-08-08 20:29:32.232][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:32.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:32.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.236][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:32.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:32.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.262][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:32.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:32.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.267][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:32.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:32.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.270][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:32.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:32.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.274][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:32.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:32.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.278][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-08 20:29:32.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-08 20:29:32.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.282][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-08 20:29:32.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-08 20:29:32.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.286][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-08 20:29:32.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-08 20:29:32.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.290][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-08 20:29:32.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-08 20:29:32.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.350][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.353][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.375][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.376][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.377][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.378][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.397][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.401][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.402][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.403][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.404][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.405][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.415][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:32.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:32.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.419][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:32.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:32.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.423][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:32.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:32.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.426][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:32.427][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:32.428][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.429][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.430][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:32.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:32.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.441][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:32.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:32.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.444][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:32.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:32.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.448][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:32.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:32.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.452][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:32.453][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:32.454][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.455][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.456][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:32.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:32.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.466][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:32.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:32.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.470][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:32.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:32.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.474][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:32.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:32.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.477][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:32.478][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:32.479][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.480][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.481][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:32.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:32.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.492][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:32.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:32.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:32.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:32.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.499][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:32.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:32.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.503][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:32.504][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:32.509][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.510][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.511][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:32.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:32.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.522][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:32.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:32.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.526][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:32.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:32.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.529][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:32.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:32.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.533][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:32.534][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:32.535][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.536][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.537][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:32.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:32.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.547][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-08 20:29:32.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:32.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.551][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-08 20:29:32.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:32.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.555][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-08 20:29:32.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:32.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.559][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-08 20:29:32.560][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:32.561][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.561][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.562][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-08 20:29:32.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:32.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.573][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:32.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:32.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.577][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:32.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:32.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.580][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:32.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:32.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.584][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:32.585][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:32.586][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.587][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.588][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:32.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:32.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.599][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:32.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:32.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.602][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:32.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:32.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.606][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:32.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:32.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.610][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:32.611][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:32.612][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.613][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.614][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:32.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:32.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.625][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:32.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:32.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.628][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:32.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:32.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.632][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:32.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:32.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.636][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:32.637][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:32.638][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.639][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.640][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:32.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:32.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.650][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:32.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:32.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.654][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:32.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:32.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.658][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:32.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:32.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.662][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:32.663][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:32.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.665][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.666][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:32.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:32.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.708][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.710][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.710][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.711][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.716][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:32.717][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:32.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.719][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.723][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:32.724][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:32.725][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.726][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.730][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:32.731][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:32.732][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.733][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.737][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:32.739][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:32.740][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.741][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.745][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:32.746][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:32.747][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.748][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.752][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:32.753][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:32.754][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.755][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.759][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:32.760][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:32.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.762][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.766][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-08 20:29:32.768][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:32.768][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.769][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.773][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:32.774][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:32.775][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.776][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.780][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:32.781][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:32.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.783][ef$get] fields variable is a list.
biodb.INFO [2025-08-08 20:29:32.790][biodb::testThat]
biodb.INFO [2025-08-08 20:29:32.791][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-08-08 20:29:32.792][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-08 20:29:32.793][biodb::testThat]
biodb.DEBUG[2025-08-08 20:29:32.806][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-08-08 20:29:32.809][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-08 20:29:32.812][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:32.819][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml.
biodb.DEBUG[2025-08-08 20:29:32.820][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:32.842][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:32.844][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:32.845][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:32.846][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:32.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:32.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:32.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:32.853][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:32.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:32.857][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.858][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.859][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.885][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:32.886][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:32.887][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.888][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.890][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:32.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:32.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.893][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:32.894][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:32.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.896][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.897][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:32.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:32.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.901][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:32.902][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:32.903][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.904][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.905][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:32.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:32.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.909][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:32.910][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:32.911][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.912][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.913][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:32.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:32.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.917][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:32.918][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:32.919][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.920][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.921][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:32.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:32.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.925][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:32.926][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:32.927][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.928][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.929][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:32.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:32.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.933][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:32.934][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:32.935][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.936][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:32.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:32.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.941][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:32.942][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:32.943][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.944][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.945][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:32.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:32.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.949][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:32.950][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:32.951][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.952][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.953][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:32.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:32.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.957][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:32.958][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:32.959][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.960][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.961][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:32.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:32.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.965][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.969][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:32.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:32.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:32.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:32.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:32.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:33.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:33.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:33.003][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-08-08 20:29:33.004][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-08-08 20:29:33.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-08-08 20:29:33.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.008][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-08-08 20:29:33.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-08-08 20:29:33.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.012][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-08-08 20:29:33.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-08-08 20:29:33.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-08 20:29:33.023][biodb::testThat]
biodb.INFO [2025-08-08 20:29:33.024][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-08-08 20:29:33.024][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-08 20:29:33.025][biodb::testThat]
biodb.TRACE[2025-08-08 20:29:33.028][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:33.029][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:33.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.031][ef$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:33.032][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-08-08 20:29:33.060][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:33.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:33.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.064][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:33.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:33.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.068][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:33.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:33.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:33.074][function(conn, opt)] With value "squalene".
sched.DEBUG[2025-08-08 20:29:33.079][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
fscache.INFO [2025-08-08 20:29:33.099][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:33.105][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/a2ed8f44d213d85be0d7e9a0448c78ad.content.
sched.DEBUG[2025-08-08 20:29:33.106][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
sched.DEBUG[2025-08-08 20:29:33.125][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 [2025-08-08 20:29:33.154][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:33.158][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/80cdc67a2a6332dd4ceb98b7656194b9.content.
sched.DEBUG[2025-08-08 20:29:33.159][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:33.161][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-08-08 20:29:33.172][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:33.173][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:33.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.175][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.176][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:33.177][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:33.178][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.179][ef$get] fields variable is a list.
biodb.INFO [2025-08-08 20:29:33.183][biodb::testThat]
biodb.INFO [2025-08-08 20:29:33.184][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-08-08 20:29:33.185][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-08 20:29:33.186][biodb::testThat]
biodb.TRACE[2025-08-08 20:29:33.210][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:33.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:33.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.220][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:33.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:33.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.224][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:33.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:33.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
sched.DEBUG[2025-08-08 20:29:33.280][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 [2025-08-08 20:29:33.283][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:33.286][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/80cdc67a2a6332dd4ceb98b7656194b9.content.
sched.DEBUG[2025-08-08 20:29:33.287][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.INFO [2025-08-08 20:29:33.301][biodb::testThat]
biodb.INFO [2025-08-08 20:29:33.302][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-08-08 20:29:33.303][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-08 20:29:33.304][biodb::testThat]
biodb.TRACE[2025-08-08 20:29:33.324][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:33.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:33.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.328][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:33.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:33.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.331][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:33.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:33.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.335][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:33.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:33.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.339][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:33.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:33.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.343][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:33.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:33.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.347][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-08 20:29:33.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-08 20:29:33.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.350][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-08 20:29:33.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-08 20:29:33.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.354][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-08 20:29:33.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-08 20:29:33.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.358][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-08 20:29:33.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-08 20:29:33.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.384][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:33.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:33.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.388][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:33.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:33.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.392][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:33.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:33.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.395][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:33.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:33.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.399][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:33.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:33.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.403][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:33.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:33.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.407][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-08 20:29:33.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-08 20:29:33.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.411][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-08 20:29:33.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-08 20:29:33.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.415][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-08 20:29:33.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-08 20:29:33.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:33.418][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-08 20:29:33.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-08 20:29:33.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:33.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-08 20:29:33.428][biodb::testThat]
biodb.INFO [2025-08-08 20:29:33.429][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-08-08 20:29:33.430][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-08 20:29:33.431][biodb::testThat]
biodb.INFO [2025-08-08 20:29:33.438][biodb::testThat]
biodb.INFO [2025-08-08 20:29:33.439][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-08-08 20:29:33.440][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-08 20:29:33.441][biodb::testThat]
biodb.INFO [2025-08-08 20:29:33.447][biodb::testThat]
biodb.INFO [2025-08-08 20:29:33.448][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-08-08 20:29:33.449][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-08 20:29:33.450][biodb::testThat]
biodb.DEBUG[2025-08-08 20:29:33.454][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
sched.TRACE[2025-08-08 20:29:34.212][try_get_rcurl_content] Using RCurl package for sending request (https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440).
biodb.INFO [2025-08-08 20:29:35.279][biodb::testThat]
biodb.INFO [2025-08-08 20:29:35.282][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-08-08 20:29:35.284][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-08 20:29:35.285][biodb::testThat]
biodb.TRACE[2025-08-08 20:29:35.295][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:35.297][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:35.298][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.300][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.301][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:35.303][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:35.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.305][ef$get] fields variable is a list.
biodb.INFO [2025-08-08 20:29:35.308][biodb::testThat]
biodb.INFO [2025-08-08 20:29:35.309][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-08-08 20:29:35.310][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-08 20:29:35.311][biodb::testThat]
biodb.TRACE[2025-08-08 20:29:35.324][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:35.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:35.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.329][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:35.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:35.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.333][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:35.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:35.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
sched.DEBUG[2025-08-08 20:29:35.454][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 [2025-08-08 20:29:35.457][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:35.461][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/80cdc67a2a6332dd4ceb98b7656194b9.content.
sched.DEBUG[2025-08-08 20:29:35.462][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
sched.DEBUG[2025-08-08 20:29:35.560][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 [2025-08-08 20:29:35.563][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:35.567][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/80cdc67a2a6332dd4ceb98b7656194b9.content.
sched.DEBUG[2025-08-08 20:29:35.568][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.TRACE[2025-08-08 20:29:35.583][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-08 20:29:35.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-08 20:29:35.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.592][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:35.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:35.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.596][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:35.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:35.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.600][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:35.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:35.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.604][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:35.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:35.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.608][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:35.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:35.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
sched.DEBUG[2025-08-08 20:29:35.620][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 [2025-08-08 20:29:35.623][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:35.625][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/8fc54eee7e982ce554bee8000d8203f7.content.
sched.DEBUG[2025-08-08 20:29:35.626][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:35.629][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:35.630][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:35.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:35.636][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:35.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:35.638][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:35.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:35.640][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-08-08 20:29:35.688][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-08 20:29:35.690][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:35.694][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml.
biodb.DEBUG[2025-08-08 20:29:35.695][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:35.696][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:35.698][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:35.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:35.700][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:35.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:35.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:35.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:35.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:35.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:35.712][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:35.713][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:35.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.715][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:35.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:35.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.728][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:35.729][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:35.730][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.731][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.732][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:35.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:35.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.737][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:35.738][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:35.739][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.740][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.741][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:35.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:35.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.746][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:35.747][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:35.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.749][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.750][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:35.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:35.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.754][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:35.755][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:35.756][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.757][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.758][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:35.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:35.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.762][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:35.764][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:35.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.766][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.767][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:35.768][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:35.769][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.770][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.771][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:35.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:35.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.776][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:35.777][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:35.778][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.779][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:35.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:35.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.785][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:35.786][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:35.787][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.788][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.790][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:35.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:35.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.794][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:35.795][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:35.796][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.797][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.799][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:35.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:35.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.803][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:35.804][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:35.805][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.806][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.807][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:35.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:35.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:35.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:35.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:35.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:35.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:35.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:35.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.824][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:35.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:35.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:35.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:35.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:35.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:35.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:35.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:35.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:35.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:35.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:35.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:35.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:35.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:35.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:35.854][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-08-08 20:29:35.865][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:35.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:35.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.870][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:35.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:35.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.874][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:35.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:35.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
sched.DEBUG[2025-08-08 20:29:35.879][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-08 20:29:35.882][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:35.885][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/6def615835d7c1dfccd5a5f135bd2f9d.content.
sched.DEBUG[2025-08-08 20:29:35.886][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:35.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:35.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:35.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:35.920][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:35.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:35.922][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:35.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:35.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:35.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:35.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.928][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:35.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:35.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.932][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:35.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:35.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:35.937][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:35.938][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:35.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:35.944][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:35.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:35.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:35.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:35.948][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-08-08 20:29:35.949][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-08 20:29:35.951][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:35.955][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml.
biodb.DEBUG[2025-08-08 20:29:35.956][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:35.958][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:35.959][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:35.961][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:35.962][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:35.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:35.968][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:35.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:35.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:35.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:35.974][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:35.975][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:35.976][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.977][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:35.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:35.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.982][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:35.984][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:35.985][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.986][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.987][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:35.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:35.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.992][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:35.993][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:35.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:35.995][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:35.996][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:35.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:35.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.001][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:36.002][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:36.003][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.004][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.005][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:36.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:36.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.009][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:36.010][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:36.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.012][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.014][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:36.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:36.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.018][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:36.019][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:36.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.021][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.022][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:36.024][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.025][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.027][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:36.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.031][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:36.032][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:36.033][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.034][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:36.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:36.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.040][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:36.041][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:36.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.043][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.044][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:36.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:36.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.049][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:36.050][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:36.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.052][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.053][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:36.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:36.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.058][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:36.059][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:36.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.061][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.062][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:36.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:36.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:36.118][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-08-08 20:29:36.119][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.123][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.128][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
sched.DEBUG[2025-08-08 20:29:36.151][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 [2025-08-08 20:29:36.154][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:36.158][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/80cdc67a2a6332dd4ceb98b7656194b9.content.
sched.DEBUG[2025-08-08 20:29:36.160][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:36.163][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:36.164][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:36.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:36.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:36.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:36.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:36.173][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.TRACE[2025-08-08 20:29:36.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.179][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.183][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:36.188][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:36.189][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:36.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:36.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:36.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:36.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:36.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:36.199][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-08-08 20:29:36.200][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-08 20:29:36.202][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:36.205][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml.
biodb.DEBUG[2025-08-08 20:29:36.206][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:36.207][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:36.208][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:36.210][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:36.211][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:36.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:36.217][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:36.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:36.219][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:36.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:36.223][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.224][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.225][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.226][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.232][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:36.233][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:36.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.235][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.236][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:36.237][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:36.238][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.239][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.241][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:36.242][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:36.243][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.244][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.245][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:36.246][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:36.247][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.248][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.249][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:36.250][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:36.251][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.252][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.260][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:36.262][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.263][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.264][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.265][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:36.266][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:36.267][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.268][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.269][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:36.270][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:36.271][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.272][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.274][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:36.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:36.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.278][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:36.279][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:36.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.281][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.282][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:36.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:36.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.286][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:36.287][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:36.288][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.289][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.291][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:36.333][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-08-08 20:29:36.334][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.338][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.343][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.351][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:36.355][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:36.356][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:36.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:36.362][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:36.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:36.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:36.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:36.366][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-08-08 20:29:36.367][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-08 20:29:36.369][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:36.373][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml.
biodb.DEBUG[2025-08-08 20:29:36.374][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:36.376][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:36.377][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:36.379][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:36.380][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:36.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:36.387][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:36.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:36.389][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:36.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:36.393][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.394][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.396][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.402][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:36.403][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:36.404][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.405][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.407][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:36.408][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:36.409][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.410][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.411][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:36.413][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:36.414][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.415][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.416][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:36.417][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:36.418][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.419][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.420][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:36.421][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:36.422][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.423][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.425][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:36.426][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.428][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.429][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:36.437][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:36.438][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.439][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.440][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:36.441][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:36.442][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.443][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.445][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:36.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:36.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.449][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:36.450][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:36.451][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.452][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.453][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:36.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:36.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.457][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:36.458][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:36.459][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.460][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.474][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:36.503][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-08-08 20:29:36.504][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.508][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.512][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.516][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:36.525][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:36.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:36.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:36.532][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:36.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:36.534][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:36.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:36.536][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-08-08 20:29:36.537][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-08 20:29:36.539][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:36.543][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml.
biodb.DEBUG[2025-08-08 20:29:36.544][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:36.545][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:36.546][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:36.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:36.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:36.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:36.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:36.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:36.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:36.558][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[2025-08-08 20:29:36.561][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.562][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.563][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.564][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.569][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:36.570][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:36.571][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.572][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.574][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:36.575][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:36.576][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.577][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.578][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:36.579][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:36.580][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.581][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.582][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:36.584][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:36.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.585][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.587][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:36.588][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:36.589][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.590][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.591][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:36.592][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.594][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.596][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:36.597][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:36.598][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.599][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.600][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:36.607][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:36.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.609][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.611][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:36.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:36.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.615][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:36.617][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:36.618][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.619][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.620][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:36.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:36.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.624][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:36.625][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:36.626][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.627][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.641][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:36.671][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-08-08 20:29:36.672][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.677][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.681][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.685][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.690][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:36.694][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:36.695][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:36.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:36.701][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:36.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:36.703][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:36.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:36.706][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-08-08 20:29:36.707][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-08 20:29:36.708][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:36.714][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml.
biodb.DEBUG[2025-08-08 20:29:36.715][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:36.716][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:36.718][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:36.720][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:36.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:36.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:36.727][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:36.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:36.729][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:36.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:36.732][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.733][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.735][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.741][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:36.742][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:36.743][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.744][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.746][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:36.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:36.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.750][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:36.751][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:36.752][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.753][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.755][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:36.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:36.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.760][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:36.761][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:36.762][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.763][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.764][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:36.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:36.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.769][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:36.770][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:36.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.772][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:36.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:36.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.778][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:36.780][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:36.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.791][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.792][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:36.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:36.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.797][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:36.798][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.799][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.800][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.801][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:36.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.806][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:36.807][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:36.808][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.809][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:36.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:36.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.815][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:36.816][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:36.817][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.818][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.819][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:36.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:36.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.824][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:36.825][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:36.826][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.827][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.828][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:36.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:36.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.832][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:36.834][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:36.835][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.836][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.837][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:36.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:36.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.846][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.854][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:36.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:36.883][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-08-08 20:29:36.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.889][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.893][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:36.897][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:36.898][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:36.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:36.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:36.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:36.906][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:36.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:36.908][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-08-08 20:29:36.909][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-08 20:29:36.910][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:36.915][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml.
biodb.DEBUG[2025-08-08 20:29:36.916][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:36.918][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:36.919][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:36.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:36.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:36.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:36.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:36.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:36.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:36.931][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[2025-08-08 20:29:36.934][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.935][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.937][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:36.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:36.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.943][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:36.944][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:36.945][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.946][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.947][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:36.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:36.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.952][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:36.953][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:36.954][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.955][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.957][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:36.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:36.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.967][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:36.969][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:36.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.970][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.972][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:36.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:36.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.976][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:36.977][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:36.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.979][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.980][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:36.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:36.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.984][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:36.986][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:36.986][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.987][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.989][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:36.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:36.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.993][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:36.994][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:36.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:36.996][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:36.998][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:36.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.002][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:37.003][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:37.004][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.005][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.007][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:37.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:37.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.011][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:37.012][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:37.013][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.014][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.016][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:37.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:37.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.020][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:37.021][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:37.022][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.023][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.025][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:37.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:37.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.029][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:37.030][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:37.031][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.032][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.034][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:37.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:37.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.038][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.043][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:37.081][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-08-08 20:29:37.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.086][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.090][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:37.095][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:37.096][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:37.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:37.102][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:37.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:37.104][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:37.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:37.107][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-08-08 20:29:37.108][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-08 20:29:37.109][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:37.114][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml.
biodb.DEBUG[2025-08-08 20:29:37.115][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:37.117][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:37.118][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:37.120][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:37.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:37.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:37.128][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:37.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:37.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:37.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:37.134][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.135][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.142][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.143][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.149][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:37.150][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:37.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.152][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.153][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:37.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:37.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.158][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:37.159][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:37.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.161][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.162][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:37.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:37.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.166][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:37.167][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:37.168][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.169][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.170][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:37.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:37.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.175][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:37.176][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:37.177][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.178][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.179][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:37.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:37.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.183][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:37.184][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:37.185][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.186][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.188][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:37.189][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.190][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.191][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.192][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:37.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.197][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:37.198][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:37.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.200][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.201][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:37.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:37.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.205][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:37.207][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:37.208][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.208][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.210][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:37.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:37.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.214][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:37.215][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:37.216][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.217][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.219][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:37.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:37.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.223][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:37.224][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:37.225][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.226][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.227][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:37.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:37.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.232][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.245][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:37.275][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-08-08 20:29:37.276][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:37.289][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:37.290][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:37.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:37.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:37.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:37.299][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:37.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:37.301][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-08-08 20:29:37.302][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-08 20:29:37.304][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:37.309][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml.
biodb.DEBUG[2025-08-08 20:29:37.310][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:37.319][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:37.321][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:37.323][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:37.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:37.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:37.330][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:37.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:37.332][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:37.333][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.TRACE[2025-08-08 20:29:37.336][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.337][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.339][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.345][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:37.346][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:37.347][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.348][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.349][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:37.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:37.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.354][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:37.355][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:37.356][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.357][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.358][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:37.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:37.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.363][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:37.364][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:37.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.366][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.368][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:37.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:37.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.372][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:37.374][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:37.375][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.376][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.377][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:37.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:37.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.382][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:37.383][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:37.384][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.385][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.387][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:37.388][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.389][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.390][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.391][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:37.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.396][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:37.397][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:37.398][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.399][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.401][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:37.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:37.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.405][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:37.406][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:37.407][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.408][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.410][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:37.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:37.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.414][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:37.415][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:37.416][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.417][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.419][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:37.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:37.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.423][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:37.424][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:37.425][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.426][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.428][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:37.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:37.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.432][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.436][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.445][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:37.475][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-08-08 20:29:37.476][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.480][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.484][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:37.496][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:37.497][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:37.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:37.503][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:37.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:37.505][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:37.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:37.507][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-08-08 20:29:37.508][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-08 20:29:37.510][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:37.514][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml.
biodb.DEBUG[2025-08-08 20:29:37.515][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:37.517][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:37.518][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:37.520][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:37.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:37.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:37.527][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:37.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:37.528][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:37.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:37.532][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.533][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.534][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.535][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.544][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:37.545][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:37.546][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.547][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.548][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:37.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:37.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.552][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:37.553][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:37.554][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.555][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.557][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:37.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:37.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.561][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:37.562][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:37.563][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.564][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.565][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:37.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:37.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.569][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:37.570][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:37.571][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.572][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.573][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:37.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:37.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.577][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:37.578][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:37.579][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.580][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.581][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:37.582][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.583][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.584][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.586][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:37.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.590][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:37.591][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:37.592][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.593][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:37.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:37.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.598][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:37.599][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:37.600][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.601][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.603][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:37.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:37.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.607][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:37.608][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:37.609][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.610][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.611][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:37.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:37.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.615][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:37.616][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:37.617][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.618][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.619][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:37.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:37.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.636][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:37.671][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-08-08 20:29:37.672][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.675][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:37.684][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:37.685][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:37.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:37.691][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:37.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:37.692][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:37.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:37.695][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-08-08 20:29:37.696][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-08 20:29:37.697][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:37.702][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml.
biodb.DEBUG[2025-08-08 20:29:37.703][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:37.705][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:37.706][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:37.708][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:37.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:37.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:37.715][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:37.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:37.717][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:37.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:37.721][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.722][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.723][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.724][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.729][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:37.730][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:37.731][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.732][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.734][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:37.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:37.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.738][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:37.739][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:37.740][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.741][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.742][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:37.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:37.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.746][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:37.747][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:37.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.749][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.750][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:37.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:37.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.755][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:37.756][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:37.757][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.758][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.759][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:37.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:37.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.763][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:37.764][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:37.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.766][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.767][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:37.768][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.769][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.770][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.772][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:37.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.776][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:37.777][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:37.778][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.779][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:37.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:37.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.784][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:37.785][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:37.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.787][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.788][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:37.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:37.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.792][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:37.793][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:37.794][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.795][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.797][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:37.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:37.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.801][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:37.802][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:37.803][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.804][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.805][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:37.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:37.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:37.854][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-08-08 20:29:37.855][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.859][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.863][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:37.866][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:37.867][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:37.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:37.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:37.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:37.874][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:37.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:37.876][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-08-08 20:29:37.877][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-08 20:29:37.879][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:37.883][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml.
biodb.DEBUG[2025-08-08 20:29:37.884][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:37.885][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:37.886][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:37.888][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:37.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:37.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:37.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:37.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:37.896][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:37.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:37.899][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.900][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.902][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.907][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:37.908][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:37.909][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.910][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.912][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:37.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:37.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.916][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:37.917][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:37.917][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.918][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.920][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:37.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:37.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.924][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:37.925][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:37.926][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.926][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.928][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:37.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:37.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.932][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:37.933][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:37.933][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.934][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.936][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:37.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:37.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.940][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:37.941][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:37.942][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.943][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.944][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:37.945][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.947][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.948][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:37.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:37.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.952][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:37.953][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:37.954][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.955][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.956][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:37.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:37.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.960][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:37.961][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:37.962][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.963][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.965][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:37.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:37.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.969][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:37.970][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:37.970][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.971][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.973][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:37.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:37.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.976][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:37.977][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:37.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.979][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.981][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:37.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:37.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.993][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:37.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:37.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:37.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:37.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:37.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:38.027][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-08-08 20:29:38.028][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:38.040][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:38.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:38.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:38.046][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:38.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:38.048][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:38.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:38.050][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-08-08 20:29:38.051][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-08 20:29:38.052][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:38.055][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml.
biodb.DEBUG[2025-08-08 20:29:38.056][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:38.057][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:38.058][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:38.060][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:38.061][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:38.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:38.066][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:38.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:38.068][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:38.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:38.071][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.072][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.074][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.080][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:38.081][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:38.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.082][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.084][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:38.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:38.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.088][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:38.089][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:38.090][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.091][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.092][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:38.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:38.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.096][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:38.097][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:38.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.099][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.100][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:38.101][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:38.102][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.103][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.104][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:38.105][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:38.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.107][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.108][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:38.109][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.110][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.111][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.112][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:38.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.116][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:38.117][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:38.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.119][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.120][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:38.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:38.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.124][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:38.125][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:38.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.127][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.129][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:38.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:38.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.132][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:38.133][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:38.134][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.135][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.137][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:38.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:38.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.141][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:38.165][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:38.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.167][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.169][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.173][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.180][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:38.208][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-08-08 20:29:38.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.213][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:38.220][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:38.221][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:38.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:38.226][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:38.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:38.228][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:38.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:38.230][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-08-08 20:29:38.231][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-08 20:29:38.233][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:38.235][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml.
biodb.DEBUG[2025-08-08 20:29:38.236][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:38.238][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:38.239][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:38.240][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:38.241][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:38.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:38.247][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:38.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:38.249][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:38.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:38.252][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.253][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.255][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.260][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:38.261][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:38.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.263][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.264][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:38.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:38.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.268][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:38.269][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:38.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.271][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.272][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:38.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:38.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.276][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:38.277][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:38.278][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.279][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.281][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:38.282][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:38.283][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.283][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.285][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:38.286][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:38.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.288][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.289][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:38.290][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.292][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.293][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:38.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.297][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:38.298][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:38.299][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.300][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:38.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:38.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.306][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:38.307][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:38.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.309][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.310][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:38.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:38.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.314][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:38.315][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:38.316][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.317][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.318][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:38.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:38.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.329][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:38.330][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:38.331][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.332][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.334][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.338][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:38.373][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-08-08 20:29:38.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:38.387][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:38.387][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:38.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:38.393][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:38.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:38.395][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:38.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:38.397][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-08-08 20:29:38.398][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-08 20:29:38.399][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:38.403][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml.
biodb.DEBUG[2025-08-08 20:29:38.404][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:38.405][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:38.407][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:38.408][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:38.409][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:38.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:38.415][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:38.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:38.416][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:38.417][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.TRACE[2025-08-08 20:29:38.420][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.421][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.422][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.423][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.428][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:38.429][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:38.430][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.431][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.432][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:38.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:38.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.436][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:38.437][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:38.438][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.439][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.441][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:38.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:38.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.445][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:38.446][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:38.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.448][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.449][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:38.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:38.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.454][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:38.455][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:38.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.457][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.458][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:38.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:38.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.462][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:38.463][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:38.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.465][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.466][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:38.467][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.468][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.469][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.471][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:38.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.475][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:38.476][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:38.477][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.478][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:38.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:38.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.483][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:38.484][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:38.485][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.486][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.493][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:38.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:38.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.498][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:38.499][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:38.500][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.501][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.502][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:38.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:38.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.506][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:38.507][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:38.508][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.509][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.511][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:38.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:38.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.518][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.526][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:38.554][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-08-08 20:29:38.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.558][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:38.566][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:38.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:38.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:38.573][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:38.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:38.575][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:38.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:38.577][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-08-08 20:29:38.578][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-08 20:29:38.579][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:38.583][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml.
biodb.DEBUG[2025-08-08 20:29:38.584][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:38.586][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:38.587][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:38.588][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:38.589][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:38.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:38.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:38.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:38.597][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:38.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:38.600][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.602][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.603][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.603][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.609][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:38.610][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:38.611][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.612][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.613][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:38.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:38.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.618][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:38.619][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:38.620][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.621][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.622][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:38.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:38.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.626][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:38.627][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:38.628][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.629][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.630][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:38.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:38.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.635][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:38.636][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:38.636][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.637][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.639][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:38.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:38.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.643][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:38.644][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:38.644][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.645][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.647][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:38.648][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.649][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.649][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.651][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:38.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.660][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:38.661][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:38.662][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.663][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.664][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:38.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:38.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.668][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:38.669][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:38.670][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.671][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.673][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:38.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:38.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.677][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:38.678][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:38.679][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.680][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.681][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:38.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:38.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.685][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:38.686][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:38.687][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.688][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.689][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:38.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:38.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.693][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.705][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:38.733][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-08-08 20:29:38.734][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.742][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:38.746][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:38.747][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:38.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:38.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:38.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:38.754][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:38.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:38.756][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-08-08 20:29:38.757][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-08 20:29:38.759][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:38.763][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml.
biodb.DEBUG[2025-08-08 20:29:38.764][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:38.765][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:38.766][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:38.768][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:38.769][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:38.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:38.775][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:38.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:38.777][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:38.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:38.780][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.781][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.783][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.788][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:38.789][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:38.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.791][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.793][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:38.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:38.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.797][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:38.798][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:38.799][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.800][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.801][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:38.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:38.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.805][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:38.806][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:38.807][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.808][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.809][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:38.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:38.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.813][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:38.814][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:38.815][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.821][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.823][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:38.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:38.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.827][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:38.828][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:38.829][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.830][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.831][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:38.832][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.833][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.834][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.835][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:38.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.839][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:38.840][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:38.841][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.842][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.844][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:38.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:38.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.848][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:38.849][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:38.850][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.851][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.852][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:38.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:38.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.856][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:38.857][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:38.858][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.859][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.861][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:38.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:38.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.865][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:38.866][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:38.867][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.868][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.869][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:38.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:38.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.874][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.885][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:38.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:38.913][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-08-08 20:29:38.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.919][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.923][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:38.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:38.927][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:38.927][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:38.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:38.933][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:38.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:38.935][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:38.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:38.937][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-08-08 20:29:38.938][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-08 20:29:38.940][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:38.944][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml.
biodb.DEBUG[2025-08-08 20:29:38.945][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:38.946][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:38.948][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:38.949][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:38.950][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:38.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:38.956][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:38.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:38.958][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:38.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:38.961][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.962][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.964][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:38.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:38.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.969][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:38.970][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:38.971][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.972][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.974][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:38.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:38.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.978][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:38.979][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:38.980][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.981][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.988][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:38.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:38.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.992][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:38.994][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:38.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:38.995][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:38.997][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:38.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:38.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.001][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:39.002][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:39.003][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.004][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.005][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:39.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:39.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.009][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:39.010][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:39.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.012][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.013][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:39.014][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.015][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.016][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.018][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:39.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.022][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:39.023][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:39.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.025][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.026][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:39.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:39.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.030][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:39.031][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:39.032][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.033][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.034][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:39.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:39.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.038][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:39.039][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:39.040][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.041][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.042][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:39.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:39.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.046][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:39.047][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:39.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.049][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.051][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:39.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:39.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.055][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:39.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:39.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.058][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:39.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:39.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:39.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:39.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:39.094][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-08-08 20:29:39.095][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.099][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.103][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:39.106][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:39.107][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:39.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:39.113][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:39.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:39.115][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:39.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:39.117][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-08-08 20:29:39.118][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-08 20:29:39.119][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:39.123][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml.
biodb.DEBUG[2025-08-08 20:29:39.125][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:39.126][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:39.127][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:39.128][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:39.129][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:39.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:39.135][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:39.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:39.137][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:39.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:39.140][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.141][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.142][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.143][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.153][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:39.154][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:39.155][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.156][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.157][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:39.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:39.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.161][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:39.162][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:39.163][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.164][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.165][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:39.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:39.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.169][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:39.170][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:39.171][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.172][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.173][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:39.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:39.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.177][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:39.178][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:39.179][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.180][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.181][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:39.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:39.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.185][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:39.186][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:39.187][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.188][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.189][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:39.190][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.191][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.192][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.193][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:39.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.197][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:39.198][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:39.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.200][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.201][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:39.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:39.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.205][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:39.206][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:39.207][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.208][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.209][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:39.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:39.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.214][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:39.215][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:39.216][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.216][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.218][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:39.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:39.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.222][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:39.223][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:39.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.225][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.226][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:39.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:39.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.230][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:39.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:39.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:39.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:39.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:39.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:39.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:39.271][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-08-08 20:29:39.273][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.277][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.281][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:39.285][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:39.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:39.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:39.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:39.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:39.293][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:39.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:39.295][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-08-08 20:29:39.296][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-08 20:29:39.298][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:39.301][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml.
biodb.DEBUG[2025-08-08 20:29:39.302][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:39.304][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:39.305][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:39.312][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:39.313][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:39.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:39.320][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:39.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:39.322][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:39.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:39.325][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.326][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.327][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.328][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.334][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:39.335][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:39.336][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.336][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.338][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:39.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:39.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.342][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:39.343][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:39.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.345][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.346][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:39.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:39.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.350][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:39.351][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:39.352][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.353][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.354][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:39.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:39.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.358][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:39.359][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:39.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.361][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.362][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:39.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:39.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.366][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:39.367][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:39.368][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.369][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.370][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:39.371][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.372][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.373][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.374][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:39.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.378][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:39.379][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:39.380][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.381][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:39.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:39.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.386][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:39.387][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:39.388][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.389][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.391][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:39.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:39.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.395][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:39.396][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:39.397][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.398][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.399][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:39.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:39.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.403][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:39.404][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:39.405][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.406][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.407][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:39.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:39.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.411][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:39.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:39.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:39.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:39.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:39.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:39.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:39.450][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-08-08 20:29:39.451][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.455][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.459][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:39.463][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:39.463][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:39.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:39.474][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:39.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:39.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:39.477][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[2025-08-08 20:29:39.478][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-08-08 20:29:39.479][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-08 20:29:39.480][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:39.484][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml.
biodb.DEBUG[2025-08-08 20:29:39.485][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:39.486][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:39.487][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:39.489][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:39.489][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:39.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:39.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:39.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:39.497][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:39.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:39.500][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.501][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.503][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.508][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:39.509][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:39.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.511][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.512][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:39.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:39.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.516][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:39.517][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:39.518][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.519][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.521][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:39.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:39.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.525][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:39.526][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:39.527][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.528][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.529][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:39.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:39.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.533][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:39.534][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:39.535][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.536][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.537][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:39.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:39.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.541][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:39.542][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:39.543][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.544][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.551][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:39.553][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.554][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.555][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.558][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:39.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.562][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:39.564][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:39.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.566][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:39.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:39.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.572][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:39.573][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:39.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.575][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.577][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:39.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:39.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.582][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:39.583][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:39.584][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.585][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.587][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:39.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:39.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.591][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:39.593][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:39.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.595][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.596][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:39.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:39.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.601][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:39.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:39.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.606][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:39.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:39.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:39.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:39.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:39.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:39.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:39.663][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-08-08 20:29:39.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.671][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.675][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
sched.DEBUG[2025-08-08 20:29:39.699][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-08 20:29:39.702][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:39.706][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/80cdc67a2a6332dd4ceb98b7656194b9.content.
sched.DEBUG[2025-08-08 20:29:39.707][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:39.710][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:39.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:39.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:39.717][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:39.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:39.720][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:39.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:39.722][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.726][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.730][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:39.735][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:39.736][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:39.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:39.741][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:39.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:39.743][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:39.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:39.746][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.750][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.762][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.771][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:39.775][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:39.776][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:39.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:39.782][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:39.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:39.783][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:39.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:39.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.802][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:39.806][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:39.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:39.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:39.812][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:39.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:39.814][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:39.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:39.816][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.824][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.828][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.837][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:39.841][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:39.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:39.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:39.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:39.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:39.849][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:39.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:39.851][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.855][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.859][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:39.862][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:39.863][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:39.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:39.869][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:39.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:39.871][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:39.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:39.873][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:39.885][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:39.885][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:39.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:39.891][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:39.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:39.893][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:39.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:39.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.899][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.903][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:39.907][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:39.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:39.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:39.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:39.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:39.915][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:39.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:39.917][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.921][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.925][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:39.929][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:39.930][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:39.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:39.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:39.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:39.937][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:39.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:39.940][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.943][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.947][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:39.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:39.952][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:39.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:39.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:39.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:39.959][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:39.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:39.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.965][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:39.973][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:39.974][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:39.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:39.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:39.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:39.982][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:39.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:39.984][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:39.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:39.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:39.998][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:40.002][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:40.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:40.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:40.009][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:40.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:40.011][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:40.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:40.013][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.017][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.021][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:40.025][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:40.025][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:40.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:40.031][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:40.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:40.033][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:40.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:40.035][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.042][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:40.046][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:40.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:40.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:40.052][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:40.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:40.054][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:40.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:40.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.060][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.064][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:40.068][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:40.069][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:40.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:40.074][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:40.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:40.076][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:40.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:40.078][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.085][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:40.089][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:40.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:40.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:40.096][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:40.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:40.097][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:40.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:40.099][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.104][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.107][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:40.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:40.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:40.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:40.118][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:40.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:40.119][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:40.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:40.121][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.125][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.129][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:40.133][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:40.134][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:40.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:40.139][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:40.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:40.141][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:40.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:40.143][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.151][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.155][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:40.159][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:40.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:40.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:40.165][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:40.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:40.167][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:40.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:40.169][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.173][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:40.180][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:40.181][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:40.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:40.187][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:40.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:40.189][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:40.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:40.191][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.195][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.198][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.216][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.224][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.229][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
sched.DEBUG[2025-08-08 20:29:40.262][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-08 20:29:40.264][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:40.267][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/63dc67d905e130c19900bd338bad7ba9.content.
sched.DEBUG[2025-08-08 20:29:40.268][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
sched.DEBUG[2025-08-08 20:29:40.271][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-08 20:29:40.274][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:40.276][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/287cac4c6e727656d926f26e3952924c.content.
sched.DEBUG[2025-08-08 20:29:40.277][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:40.280][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:40.281][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:40.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:40.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:40.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:40.288][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:40.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:40.290][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-08-08 20:29:40.291][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-08 20:29:40.292][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:40.296][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml.
biodb.DEBUG[2025-08-08 20:29:40.297][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:40.299][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:40.300][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:40.301][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:40.302][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:40.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:40.313][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:40.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:40.314][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:40.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:40.318][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:40.319][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:40.319][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.320][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:40.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:40.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.325][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:40.326][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:40.327][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.328][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.330][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:40.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:40.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.333][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:40.334][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:40.335][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.336][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.338][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:40.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:40.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.342][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:40.343][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:40.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.345][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.346][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:40.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:40.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.350][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:40.351][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:40.352][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.353][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.354][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:40.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:40.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.358][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:40.359][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:40.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.361][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.362][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:40.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:40.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.366][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:40.367][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.368][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.369][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.370][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:40.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.374][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.375][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.376][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.377][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.378][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.382][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:40.383][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:40.384][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.385][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.386][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:40.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:40.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.390][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:40.391][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:40.392][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.393][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.394][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:40.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:40.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.398][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:40.399][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:40.400][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.401][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.402][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:40.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:40.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.406][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:40.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:40.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:40.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:40.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:40.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:40.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.418][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:40.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:40.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:40.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:40.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:40.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:40.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:40.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:40.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:40.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:40.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:40.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:40.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:40.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:40.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:40.445][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-08-08 20:29:40.446][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.450][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:40.463][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:40.464][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:40.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:40.469][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:40.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:40.471][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:40.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:40.473][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.477][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.481][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:40.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:40.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:40.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:40.491][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:40.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:40.493][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:40.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:40.495][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-08-08 20:29:40.496][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-08 20:29:40.497][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:40.501][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml.
biodb.DEBUG[2025-08-08 20:29:40.502][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:40.503][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:40.504][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:40.506][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:40.507][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:40.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:40.512][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:40.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:40.514][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:40.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:40.517][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:40.519][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:40.519][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.520][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:40.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:40.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.526][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:40.527][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:40.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.529][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.530][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:40.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:40.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.534][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:40.535][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:40.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.537][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.538][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:40.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:40.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.542][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:40.543][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:40.544][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.545][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.547][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:40.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:40.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.551][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:40.552][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:40.553][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.554][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.555][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:40.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:40.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.559][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:40.560][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:40.561][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.562][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.563][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:40.564][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.566][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.568][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:40.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:40.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.572][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.573][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.575][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.580][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:40.581][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:40.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.583][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.585][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:40.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:40.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.589][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:40.590][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:40.591][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.592][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.594][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:40.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:40.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.598][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:40.599][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:40.600][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.601][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.602][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:40.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:40.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.606][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:40.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:40.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:40.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:40.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:40.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:40.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.619][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:40.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:40.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:40.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:40.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:40.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:40.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:40.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:40.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:40.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:40.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:40.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:40.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:40.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:40.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:40.654][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-08-08 20:29:40.655][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.664][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
sched.DEBUG[2025-08-08 20:29:40.688][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-08 20:29:40.691][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:40.694][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/80cdc67a2a6332dd4ceb98b7656194b9.content.
sched.DEBUG[2025-08-08 20:29:40.696][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:40.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:40.700][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:40.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:40.707][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:40.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:40.709][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:40.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:40.711][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.715][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.719][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:40.723][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:40.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:40.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:40.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:40.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:40.732][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:40.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:40.734][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.742][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.750][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:40.754][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:40.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:40.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:40.761][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:40.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:40.763][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:40.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:40.765][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:40.785][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:40.786][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:40.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:40.799][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:40.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:40.802][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:40.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:40.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.813][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:40.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:40.825][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:40.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:40.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:40.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:40.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:40.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:40.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.838][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:40.846][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:40.847][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:40.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:40.853][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:40.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:40.854][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:40.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:40.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.864][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:40.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:40.869][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:40.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:40.874][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:40.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:40.876][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:40.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:40.878][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.882][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:40.890][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:40.890][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:40.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:40.896][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:40.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:40.897][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:40.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:40.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.903][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.907][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:40.911][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:40.912][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:40.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:40.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:40.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:40.920][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:40.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:40.922][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.926][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:40.934][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:40.935][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:40.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:40.940][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:40.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:40.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:40.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:40.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.948][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:40.964][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:40.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:40.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:40.970][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:40.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:40.972][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:40.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:40.974][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.978][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:40.982][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:40.986][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:40.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:40.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:40.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:40.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:40.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:40.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:40.996][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:40.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:40.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.007][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.013][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.015][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.017][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.021][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.028][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.029][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.036][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.038][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.042][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.046][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.050][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.051][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.058][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.060][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.081][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.085][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.089][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.093][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.093][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.100][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.102][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.115][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.119][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.119][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.125][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.127][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.129][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.136][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.140][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.141][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.148][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.158][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.162][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.163][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.170][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.180][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
sched.DEBUG[2025-08-08 20:29:41.199][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-08 20:29:41.202][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:41.205][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/80cdc67a2a6332dd4ceb98b7656194b9.content.
sched.DEBUG[2025-08-08 20:29:41.206][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:41.210][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.210][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.216][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.217][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.219][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.227][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.231][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.232][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.237][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.239][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.245][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.249][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.253][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.257][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.261][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.262][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.272][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.274][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.287][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.291][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.295][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.296][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.301][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.309][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.317][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.321][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.325][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.331][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.333][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.335][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.339][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.343][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.347][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.348][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.353][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.357][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.361][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.365][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.369][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.369][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.377][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.387][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.391][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.391][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.397][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.399][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.401][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.405][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.413][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.414][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.424][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.427][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.429][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.433][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.440][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.441][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.449][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.455][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.458][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.463][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.469][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.470][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.473][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.477][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.484][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.492][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.498][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.502][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.506][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.507][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.512][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.514][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.516][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.520][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.524][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.528][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.528][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.534][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.536][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.542][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.545][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.549][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.550][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.559][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.563][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.570][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.584][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.586][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.588][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.592][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.600][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.600][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.607][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.613][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.617][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.621][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.622][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.627][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.629][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.631][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.643][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.644][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.649][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.651][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.653][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.657][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.679][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.683][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:41.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.701][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-08 20:29:41.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-08 20:29:41.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-08 20:29:41.712][biodb::testThat]
biodb.INFO [2025-08-08 20:29:41.714][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-08-08 20:29:41.715][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-08 20:29:41.716][biodb::testThat]
biodb.TRACE[2025-08-08 20:29:41.718][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-08 20:29:41.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-08 20:29:41.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.722][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:41.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:41.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.726][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:41.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:41.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.730][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:41.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:41.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.734][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:41.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:41.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.747][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.748][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.754][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.756][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-08-08 20:29:41.759][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-08 20:29:41.762][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:41.764][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/8fc54eee7e982ce554bee8000d8203f7.content.
sched.DEBUG[2025-08-08 20:29:41.765][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:41.767][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.768][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.773][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.775][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.777][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:41.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:41.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.781][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:41.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:41.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.785][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:41.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:41.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
sched.DEBUG[2025-08-08 20:29:41.789][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-08 20:29:41.792][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:41.794][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/6def615835d7c1dfccd5a5f135bd2f9d.content.
sched.DEBUG[2025-08-08 20:29:41.795][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:41.797][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.806][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.808][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:41.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:41.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.812][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:41.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:41.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.816][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:41.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:41.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.820][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.821][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.826][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.830][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:41.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:41.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.834][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:41.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:41.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:41.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:41.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:41.842][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-08 20:29:41.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.849][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.851][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.857][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.861][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:41.862][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-08 20:29:41.863][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-08 20:29:41.864][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-08 20:29:41.865][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:41.866][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.867][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.868][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.869][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.870][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.871][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.872][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.873][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.874][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:41.875][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:41.876][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.877][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.878][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.879][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.880][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-08 20:29:41.881][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.885][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.889][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.908][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-08-08 20:29:41.910][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.910][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.916][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.918][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.920][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.928][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:41.929][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-08 20:29:41.930][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-08 20:29:41.931][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-08 20:29:41.932][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:41.933][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.934][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.935][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.935][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.936][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.938][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.940][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.941][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:41.942][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:41.943][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.944][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.945][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.945][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.946][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-08 20:29:41.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.955][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.960][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-08 20:29:41.961][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:41.962][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:41.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:41.968][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:41.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:41.970][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:41.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:41.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.981][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:41.982][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-08 20:29:41.982][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-08 20:29:41.983][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-08 20:29:41.984][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:41.985][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.986][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.987][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.988][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.989][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.990][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.991][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.992][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.993][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:41.994][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:41.995][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.996][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:41.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:41.998][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:41.999][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-08 20:29:42.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.004][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.008][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.012][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-08-08 20:29:42.013][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-08 20:29:42.014][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-08 20:29:42.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.031][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:42.104][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:42.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:42.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:42.111][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:42.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:42.113][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:42.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-08-08 20:29:42.116][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-08 20:29:42.119][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:42.121][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/2e865a03592d6effdf242ff63104f35a.content.
sched.DEBUG[2025-08-08 20:29:42.122][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
sched.DEBUG[2025-08-08 20:29:42.125][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-08 20:29:42.127][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:42.130][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/f0c73645ca32490f91d503a462d812b2.content.
sched.DEBUG[2025-08-08 20:29:42.131][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:42.133][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:42.134][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:42.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:42.139][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:42.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:42.141][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:42.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:42.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.147][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:42.154][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:42.155][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:42.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:42.160][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:42.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:42.162][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:42.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:42.164][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.168][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:42.176][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:42.176][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:42.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:42.182][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:42.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:42.184][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:42.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:42.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.193][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:42.226][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-08 20:29:42.249][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:42.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:42.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:42.256][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:42.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:42.258][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:42.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:42.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.267][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.268][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-08 20:29:42.269][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-08 20:29:42.270][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-08 20:29:42.271][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.272][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.273][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.275][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.276][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.277][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.278][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.279][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.280][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.281][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.282][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.283][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.285][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.286][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-08 20:29:42.287][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.291][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.299][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-08-08 20:29:42.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:42.301][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:42.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:42.306][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:42.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:42.308][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:42.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:42.322][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.356][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.357][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-08 20:29:42.358][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-08 20:29:42.359][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-08 20:29:42.360][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.361][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.362][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.363][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.364][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.365][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.366][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.367][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.368][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.369][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.379][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.380][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.382][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.382][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.383][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.384][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-08 20:29:42.386][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.390][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.398][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-08 20:29:42.399][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:42.400][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:42.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:42.405][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:42.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:42.407][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:42.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:42.409][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.413][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.417][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.418][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-08 20:29:42.419][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-08 20:29:42.420][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-08 20:29:42.420][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.421][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.422][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.423][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.424][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.425][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.426][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.428][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.429][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.430][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.431][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.432][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.433][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.434][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.435][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-08 20:29:42.436][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.444][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.448][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-08-08 20:29:42.449][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-08 20:29:42.450][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-08 20:29:42.458][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-08 20:29:42.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-08 20:29:42.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-08 20:29:42.465][biodb::testThat]
biodb.INFO [2025-08-08 20:29:42.467][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-08-08 20:29:42.467][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-08 20:29:42.468][biodb::testThat]
biodb.TRACE[2025-08-08 20:29:42.471][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-08 20:29:42.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-08 20:29:42.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:42.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:42.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.479][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:42.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:42.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.483][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:42.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:42.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.487][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:42.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:42.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:42.499][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:42.500][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:42.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:42.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:42.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:42.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:42.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-08-08 20:29:42.510][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-08 20:29:42.513][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:42.515][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/8fc54eee7e982ce554bee8000d8203f7.content.
sched.DEBUG[2025-08-08 20:29:42.516][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:42.518][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:42.519][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:42.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:42.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:42.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:42.526][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:42.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:42.528][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:42.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:42.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.532][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:42.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:42.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.536][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:42.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:42.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
sched.DEBUG[2025-08-08 20:29:42.541][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-08 20:29:42.543][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:42.545][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/6def615835d7c1dfccd5a5f135bd2f9d.content.
sched.DEBUG[2025-08-08 20:29:42.546][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:42.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:42.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:42.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:42.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:42.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:42.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:42.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:42.559][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:42.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:42.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:42.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:42.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.567][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:42.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:42.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:42.571][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:42.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:42.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:42.577][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:42.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:42.579][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:42.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:42.581][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:42.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:42.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.585][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:42.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:42.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.589][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:42.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:42.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:42.593][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-08 20:29:42.594][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:42.595][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:42.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:42.601][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:42.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:42.603][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:42.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:42.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.609][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.613][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.614][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-08 20:29:42.614][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-08 20:29:42.615][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-08 20:29:42.616][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.617][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.618][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.620][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.621][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.622][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.623][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.624][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.625][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.626][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.627][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.628][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.629][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.630][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.631][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-08 20:29:42.632][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.636][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.640][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.644][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-08-08 20:29:42.645][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:42.646][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:42.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:42.657][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:42.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:42.659][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:42.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:42.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.665][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.669][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.670][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-08 20:29:42.671][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-08 20:29:42.671][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-08 20:29:42.672][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.673][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.674][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.675][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.676][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.677][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.678][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.679][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.680][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.681][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.682][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.683][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.684][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.685][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.686][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.687][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-08 20:29:42.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.692][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.695][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.700][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-08 20:29:42.701][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:42.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:42.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:42.708][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:42.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:42.710][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:42.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:42.713][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.717][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.721][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.722][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-08 20:29:42.723][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-08 20:29:42.724][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-08 20:29:42.725][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.726][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.727][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.728][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.729][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.730][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.731][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.732][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.733][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.734][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.735][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.736][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.737][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.738][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.739][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.740][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-08 20:29:42.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.745][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.749][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.753][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-08-08 20:29:42.754][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-08 20:29:42.755][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-08 20:29:42.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:42.783][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:42.784][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:42.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:42.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:42.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:42.792][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:42.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-08-08 20:29:42.795][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-08 20:29:42.798][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:42.800][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/2e865a03592d6effdf242ff63104f35a.content.
sched.DEBUG[2025-08-08 20:29:42.801][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
sched.DEBUG[2025-08-08 20:29:42.804][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-08 20:29:42.806][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:42.809][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/f0c73645ca32490f91d503a462d812b2.content.
sched.DEBUG[2025-08-08 20:29:42.815][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:42.818][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:42.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:42.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:42.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:42.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:42.826][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:42.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:42.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:42.840][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:42.840][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:42.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:42.846][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:42.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:42.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:42.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:42.850][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.858][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:42.862][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:42.863][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:42.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:42.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:42.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:42.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:42.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:42.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.876][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:42.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:42.885][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-08 20:29:42.886][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:42.887][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:42.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:42.892][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:42.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:42.894][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:42.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:42.896][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.900][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.904][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.905][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-08 20:29:42.906][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-08 20:29:42.907][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-08 20:29:42.908][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.909][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.910][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.911][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.912][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.913][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.914][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.915][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.915][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.916][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.917][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.918][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.919][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.920][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.921][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.922][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-08 20:29:42.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.931][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.935][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-08-08 20:29:42.936][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:42.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:42.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:42.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:42.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:42.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:42.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:42.946][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.950][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.954][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.955][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-08 20:29:42.956][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-08 20:29:42.957][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-08 20:29:42.958][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.959][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.960][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.961][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.962][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.963][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.969][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.970][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.971][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.972][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.973][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:42.974][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.975][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.976][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.977][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.978][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-08 20:29:42.979][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.983][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:42.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:42.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:42.991][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-08 20:29:42.992][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:42.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:42.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:42.999][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:43.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:43.000][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:43.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:43.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.011][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.012][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-08 20:29:43.012][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-08 20:29:43.013][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-08 20:29:43.014][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.015][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.016][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.017][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.018][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.019][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.020][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.022][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.023][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.024][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.025][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.026][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.027][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.028][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.029][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-08 20:29:43.030][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.037][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.041][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-08-08 20:29:43.042][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-08 20:29:43.043][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-08 20:29:43.051][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-08 20:29:43.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-08 20:29:43.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-08 20:29:43.058][biodb::testThat]
biodb.INFO [2025-08-08 20:29:43.059][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-08-08 20:29:43.059][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-08 20:29:43.060][biodb::testThat]
biodb.TRACE[2025-08-08 20:29:43.063][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-08 20:29:43.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-08 20:29:43.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.067][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.071][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.074][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.078][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:43.086][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:43.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:43.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:43.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:43.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:43.094][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:43.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-08-08 20:29:43.097][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-08 20:29:43.100][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:43.102][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/8fc54eee7e982ce554bee8000d8203f7.content.
sched.DEBUG[2025-08-08 20:29:43.103][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:43.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:43.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:43.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:43.111][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:43.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:43.113][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:43.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:43.115][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.124][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.128][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
sched.DEBUG[2025-08-08 20:29:43.133][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-08 20:29:43.135][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:43.137][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/6def615835d7c1dfccd5a5f135bd2f9d.content.
sched.DEBUG[2025-08-08 20:29:43.138][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:43.141][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:43.141][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:43.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:43.147][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:43.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:43.149][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:43.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:43.151][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.155][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.159][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:43.163][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:43.163][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:43.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:43.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:43.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:43.171][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:43.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:43.173][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.181][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:43.185][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-08 20:29:43.186][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:43.187][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:43.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:43.192][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:43.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:43.194][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:43.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:43.196][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.204][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.205][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-08 20:29:43.206][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-08 20:29:43.207][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-08 20:29:43.207][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.208][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.209][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.211][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.212][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.213][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.214][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.215][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.216][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.217][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.218][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.219][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.220][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.221][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.222][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-08 20:29:43.223][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.227][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.230][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.235][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-08-08 20:29:43.236][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:43.236][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:43.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:43.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:43.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:43.244][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:43.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:43.246][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.250][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.254][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.255][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-08 20:29:43.255][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-08 20:29:43.256][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-08 20:29:43.257][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.258][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.259][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.261][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.262][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.263][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.264][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.265][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.266][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.267][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.268][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.269][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.276][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.277][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-08 20:29:43.279][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.283][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.287][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.291][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-08 20:29:43.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:43.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:43.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:43.299][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:43.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:43.300][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:43.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:43.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.310][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.311][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-08 20:29:43.312][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-08 20:29:43.313][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-08 20:29:43.314][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.315][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.316][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.317][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.318][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.319][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.320][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.321][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.322][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.323][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.324][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.325][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.326][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.327][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.328][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.328][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-08 20:29:43.330][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.337][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.341][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-08-08 20:29:43.342][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-08 20:29:43.343][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-08 20:29:43.361][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.365][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.369][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:43.381][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:43.381][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:43.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:43.387][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:43.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:43.389][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:43.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-08-08 20:29:43.392][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-08 20:29:43.395][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:43.396][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/2e865a03592d6effdf242ff63104f35a.content.
sched.DEBUG[2025-08-08 20:29:43.397][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
sched.DEBUG[2025-08-08 20:29:43.400][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
fscache.INFO [2025-08-08 20:29:43.403][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:43.405][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/f0c73645ca32490f91d503a462d812b2.content.
sched.DEBUG[2025-08-08 20:29:43.406][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:43.408][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:43.409][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:43.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:43.415][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:43.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:43.417][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:43.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:43.419][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.422][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:43.436][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:43.436][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:43.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:43.442][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:43.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:43.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:43.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:43.446][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.453][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:43.457][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:43.458][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:43.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:43.463][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:43.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:43.465][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:43.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:43.467][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.471][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.475][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:43.479][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-08 20:29:43.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:43.481][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:43.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:43.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:43.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:43.488][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:43.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:43.490][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.498][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.499][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-08 20:29:43.500][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-08 20:29:43.501][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-08 20:29:43.502][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.503][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.504][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.504][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.505][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.506][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.507][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.508][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.509][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.510][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.511][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.512][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.513][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.515][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.516][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-08 20:29:43.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.529][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-08-08 20:29:43.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:43.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:43.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:43.537][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:43.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:43.538][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:43.539][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".
biodb.TRACE[2025-08-08 20:29:43.541][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.545][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.548][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.549][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-08 20:29:43.550][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-08 20:29:43.551][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-08 20:29:43.552][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.553][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.554][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.555][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.556][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.557][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.558][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.559][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.560][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.561][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.562][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.563][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.564][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.566][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.566][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-08 20:29:43.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.575][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.584][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-08 20:29:43.586][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:43.587][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:43.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:43.592][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:43.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:43.594][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:43.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:43.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.603][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.604][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-08 20:29:43.605][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-08 20:29:43.606][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-08 20:29:43.607][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.608][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.609][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.610][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.611][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.612][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.613][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.614][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.615][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.616][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.617][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-08 20:29:43.618][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.619][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.620][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.621][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-08 20:29:43.622][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.626][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.634][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-08-08 20:29:43.635][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-08 20:29:43.636][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-08 20:29:43.653][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-08 20:29:43.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-08 20:29:43.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-08 20:29:43.660][biodb::testThat]
biodb.INFO [2025-08-08 20:29:43.661][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2025-08-08 20:29:43.662][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-08 20:29:43.663][biodb::testThat]
biodb.DEBUG[2025-08-08 20:29:43.665][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-08-08 20:29:43.666][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-08 20:29:43.667][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:43.670][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml.
biodb.DEBUG[2025-08-08 20:29:43.671][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:43.672][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:43.673][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:43.675][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:43.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:43.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:43.681][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:43.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:43.683][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:43.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:43.686][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:43.687][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:43.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.689][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:43.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:43.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.694][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:43.695][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:43.696][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.697][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.698][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:43.699][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:43.700][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.701][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.702][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:43.703][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:43.704][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.705][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.706][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:43.707][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:43.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.709][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.711][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:43.712][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:43.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.713][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.715][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:43.716][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.717][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.719][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.720][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.721][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.722][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.723][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:43.724][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:43.725][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.726][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.727][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:43.728][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:43.729][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.734][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.736][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:43.737][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:43.738][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.739][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.744][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:43.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:43.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.752][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:43.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:43.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:43.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:43.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:43.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:43.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:43.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:43.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:43.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:43.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:43.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:43.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:43.779][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-08-08 20:29:43.780][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-08-08 20:29:43.787][biodb::testThat]
biodb.INFO [2025-08-08 20:29:43.789][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-08-08 20:29:43.790][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-08 20:29:43.791][biodb::testThat]
biodb.DEBUG[2025-08-08 20:29:43.799][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-08-08 20:29:43.800][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-08-08 20:29:43.801][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
fscache.INFO [2025-08-08 20:29:43.803][cch$loadContents] Load 3 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:43.805][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml.
fscache.DEBUG[2025-08-08 20:29:43.808][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml.
fscache.DEBUG[2025-08-08 20:29:43.812][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml.
biodb.DEBUG[2025-08-08 20:29:43.813][conn$getEntryContent] 3 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:43.815][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-08-08 20:29:43.816][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:43.817][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:43.818][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:43.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:43.823][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:43.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:43.825][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:43.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:43.828][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:43.829][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:43.830][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.831][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:43.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:43.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.836][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:43.837][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:43.838][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.839][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.840][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:43.841][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:43.842][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.843][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.844][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:43.845][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:43.846][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.847][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.848][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:43.849][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:43.850][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.851][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.852][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:43.853][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:43.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.855][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.857][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:43.858][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.859][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.861][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.862][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.863][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.864][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.865][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:43.866][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:43.867][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.868][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.869][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:43.870][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:43.871][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.872][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.873][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:43.874][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:43.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.876][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.881][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:43.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:43.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.896][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:43.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:43.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:43.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:43.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:43.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:43.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:43.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:43.911][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:43.912][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:43.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:43.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:43.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:43.919][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:43.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:43.923][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:43.924][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:43.925][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.926][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:43.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:43.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.931][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:43.932][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:43.933][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.934][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.935][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:43.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:43.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.939][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:43.940][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:43.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.942][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.943][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:43.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:43.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.947][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:43.949][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:43.950][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.950][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.952][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:43.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:43.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.956][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:43.957][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:43.958][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.959][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.960][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:43.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:43.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.964][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:43.965][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:43.966][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.967][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.968][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:43.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:43.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.972][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:43.973][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.974][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.975][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.976][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:43.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:43.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.980][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.981][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.982][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.983][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.984][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:43.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.988][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:43.989][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:43.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.991][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.993][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:43.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:43.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:43.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:43.997][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:43.998][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:43.999][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.000][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.001][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:44.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:44.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.005][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:44.006][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:44.007][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.008][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.009][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:44.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:44.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:44.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:44.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.017][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:44.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:44.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:44.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:44.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.025][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:44.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:44.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:44.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:44.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:44.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:44.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:44.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:44.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:44.046][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:44.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:44.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:44.053][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:44.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:44.055][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:44.058][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:44.059][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:44.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.061][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:44.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:44.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.066][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:44.067][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:44.068][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.069][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.070][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:44.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:44.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.074][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:44.075][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:44.076][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.077][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.078][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:44.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:44.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.082][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:44.083][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:44.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.085][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.086][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:44.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:44.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.090][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:44.091][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:44.092][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.093][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.094][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:44.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:44.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.098][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:44.099][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:44.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.101][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.102][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:44.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:44.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.106][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:44.107][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:44.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.109][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.110][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:44.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:44.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.114][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:44.115][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:44.116][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.117][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.118][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:44.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:44.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.122][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:44.123][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:44.124][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.125][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.127][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:44.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:44.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.131][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:44.132][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:44.133][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.133][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.135][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:44.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:44.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.139][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:44.140][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:44.140][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.141][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.143][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:44.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:44.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.147][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:44.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:44.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.150][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:44.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:44.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:44.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:44.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.158][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:44.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:44.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:44.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:44.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:44.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:44.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:44.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:44.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:44.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:44.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:44.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:44.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:44.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:44.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:44.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:44.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:44.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:44.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:44.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:44.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:44.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:44.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:44.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:44.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:44.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:44.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:44.217][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-08-08 20:29:44.218][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-08-08 20:29:44.219][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-08-08 20:29:44.232][biodb::testThat]
biodb.INFO [2025-08-08 20:29:44.233][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2025-08-08 20:29:44.234][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-08 20:29:44.235][biodb::testThat]
biodb.INFO [2025-08-08 20:29:44.258][biodb::testThat]
biodb.INFO [2025-08-08 20:29:44.259][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2025-08-08 20:29:44.260][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-08 20:29:44.261][biodb::testThat]
biodb.INFO [2025-08-08 20:29:44.268][biodb::testThat]
biodb.INFO [2025-08-08 20:29:44.269][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2025-08-08 20:29:44.270][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-08 20:29:44.271][biodb::testThat]
sched.DEBUG[2025-08-08 20:29:44.274][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
fscache.INFO [2025-08-08 20:29:44.276][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:44.282][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/02ece1564def26723013d564c4071584.content.
sched.DEBUG[2025-08-08 20:29:44.283][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.TRACE[2025-08-08 20:29:44.293][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:44.295][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:44.296][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.297][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:44.298][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:44.299][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:44.300][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:44.301][ef$get] fields variable is a list.
biodb.INFO [2025-08-08 20:29:44.302][biodb::testThat]
biodb.INFO [2025-08-08 20:29:44.303][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2025-08-08 20:29:44.304][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-08 20:29:44.305][biodb::testThat]
biodb.ERROR[2025-08-08 20:29:44.318][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-08-08 20:29:44.332][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-08-08 20:29:44.344][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-08-08 20:29:44.345][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-08 20:29:44.346][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-08 20:29:44.352][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:44.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:44.354][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:44.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:44.356][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-08 20:29:44.367][biodb::testContext]
biodb.INFO [2025-08-08 20:29:44.368][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-08 20:29:44.369][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-08-08 20:29:44.370][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-08 20:29:44.371][biodb::testContext]
biodb.INFO [2025-08-08 20:29:44.373][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-08-08 20:29:44.374][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-08-08 20:29:44.378][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-08 20:29:44.379][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-08 20:29:44.380][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-08 20:29:44.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.384][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-08 20:29:44.385][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-08 20:29:44.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.388][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-08 20:29:44.389][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-08 20:29:44.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.392][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.DEBUG[2025-08-08 20:29:44.393][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-08 20:29:44.394][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-08 20:29:44.395][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-08 20:29:44.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.398][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-08 20:29:44.399][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-08 20:29:44.400][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-08 20:29:44.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.404][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-08 20:29:44.405][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-08 20:29:44.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.408][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-08 20:29:44.409][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-08 20:29:44.410][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-08 20:29:44.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.414][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-08 20:29:44.415][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-08 20:29:44.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.418][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-08 20:29:44.419][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-08 20:29:44.420][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-08 20:29:44.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.423][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[2025-08-08 20:29:44.424][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-08 20:29:44.425][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-08 20:29:44.426][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-08 20:29:44.427][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-08 20:29:44.428][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-08 20:29:44.429][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-08 20:29:44.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.432][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-08 20:29:44.433][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-08 20:29:44.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.437][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-08 20:29:44.438][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-08 20:29:44.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.441][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-08 20:29:44.442][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-08 20:29:44.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.445][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[2025-08-08 20:29:44.446][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-08 20:29:44.447][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-08 20:29:44.448][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-08 20:29:44.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.451][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-08 20:29:44.452][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-08 20:29:44.456][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-08 20:29:44.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.458][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[2025-08-08 20:29:44.459][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-08 20:29:44.460][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-08 20:29:44.461][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-08 20:29:44.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.465][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-08 20:29:44.467][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:44.468][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-08 20:29:44.469][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:44.470][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-08 20:29:44.471][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:44.472][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-08 20:29:44.473][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:44.474][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-08 20:29:44.475][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-08 20:29:44.476][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-08 20:29:44.477][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:44.478][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-08 20:29:44.479][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-08 20:29:44.480][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:44.481][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:44.482][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-08 20:29:44.482][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-08 20:29:44.482][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-08 20:29:44.482][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-08 20:29:44.482][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-08 20:29:44.483][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-08 20:29:44.483][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:44.484][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:44.485][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-08 20:29:44.486][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:44.487][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:44.488][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-08 20:29:44.489][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:44.490][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-08 20:29:44.491][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-08 20:29:44.492][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:44.493][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:44.494][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-08 20:29:44.496][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:44.502][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-08 20:29:44.504][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:44.505][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-08 20:29:44.506][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:44.507][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-08 20:29:44.508][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:44.509][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-08 20:29:44.510][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-08 20:29:44.511][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-08 20:29:44.512][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:44.513][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-08 20:29:44.514][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-08 20:29:44.515][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:44.516][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:44.517][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-08 20:29:44.517][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-08 20:29:44.517][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-08 20:29:44.517][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-08 20:29:44.517][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-08 20:29:44.518][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-08 20:29:44.519][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:44.519][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:44.520][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-08 20:29:44.521][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:44.522][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:44.523][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-08 20:29:44.524][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:44.525][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-08 20:29:44.526][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-08 20:29:44.527][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:44.528][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:44.529][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-08 20:29:44.531][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:44.531][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-08 20:29:44.532][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:44.533][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-08 20:29:44.534][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:44.535][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-08 20:29:44.536][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:44.537][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-08 20:29:44.538][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-08 20:29:44.539][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-08 20:29:44.540][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:44.541][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-08 20:29:44.542][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-08 20:29:44.543][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:44.544][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:44.545][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:44.546][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-08 20:29:44.547][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:44.548][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:44.549][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-08 20:29:44.550][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:44.551][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:44.552][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-08 20:29:44.552][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:44.553][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-08 20:29:44.554][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-08 20:29:44.555][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:44.556][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:44.558][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-08 20:29:44.559][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:44.560][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-08 20:29:44.561][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:44.562][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-08 20:29:44.563][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:44.564][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-08 20:29:44.565][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:44.566][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-08 20:29:44.568][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-08 20:29:44.569][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-08 20:29:44.570][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:44.571][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-08 20:29:44.572][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-08 20:29:44.573][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:44.574][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:44.575][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:44.576][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-08 20:29:44.577][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:44.577][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:44.578][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-08 20:29:44.579][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:44.580][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:44.581][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-08 20:29:44.582][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:44.583][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-08 20:29:44.584][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-08 20:29:44.585][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:44.586][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:44.588][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-08 20:29:44.588][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.589][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[2025-08-08 20:29:44.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:44.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:44.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.594][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[2025-08-08 20:29:44.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:44.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:44.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:44.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:44.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:44.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:44.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:44.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:44.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:44.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:44.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.616][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[2025-08-08 20:29:44.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:44.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:44.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.620][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[2025-08-08 20:29:44.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:44.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:44.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:44.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:44.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:44.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:44.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:44.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:44.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:44.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:44.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:44.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:44.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.651][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[2025-08-08 20:29:44.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:44.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:44.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.656][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[2025-08-08 20:29:44.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:44.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:44.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:44.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:44.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.664][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[2025-08-08 20:29:44.665][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-08 20:29:44.666][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-08 20:29:44.668][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-08 20:29:44.669][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-08 20:29:44.670][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-08 20:29:44.672][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-08 20:29:44.673][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-08 20:29:44.674][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-08 20:29:44.676][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-08 20:29:44.677][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-08 20:29:44.679][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-08 20:29:44.680][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-08 20:29:44.681][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-08 20:29:44.683][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-08 20:29:44.684][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-08 20:29:44.685][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-08 20:29:44.687][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-08 20:29:44.688][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-08 20:29:44.689][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-08 20:29:44.691][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-08 20:29:44.692][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-08 20:29:44.693][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-08 20:29:44.695][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-08 20:29:44.696][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-08 20:29:44.698][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-08 20:29:44.699][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-08 20:29:44.700][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-08 20:29:44.702][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-08 20:29:44.703][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-08 20:29:44.704][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-08 20:29:44.706][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-08 20:29:44.707][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-08 20:29:44.708][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-08 20:29:44.710][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-08 20:29:44.711][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-08 20:29:44.712][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-08 20:29:44.714][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-08 20:29:44.715][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-08 20:29:44.716][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-08 20:29:44.718][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-08 20:29:44.719][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-08 20:29:44.721][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-08 20:29:44.722][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-08 20:29:44.723][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-08 20:29:44.725][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-08 20:29:44.726][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-08 20:29:44.727][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-08 20:29:44.729][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-08 20:29:44.730][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-08 20:29:44.731][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-08 20:29:44.733][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-08 20:29:44.734][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-08 20:29:44.735][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-08 20:29:44.737][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-08 20:29:44.738][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-08 20:29:44.739][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-08 20:29:44.741][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-08 20:29:44.742][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-08 20:29:44.744][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-08 20:29:44.745][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-08 20:29:44.746][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-08 20:29:44.748][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-08 20:29:44.749][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-08 20:29:44.750][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-08 20:29:44.752][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-08 20:29:44.753][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-08 20:29:44.754][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-08 20:29:44.756][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-08 20:29:44.757][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-08 20:29:44.759][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-08 20:29:44.760][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-08 20:29:44.761][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-08 20:29:44.763][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-08 20:29:44.764][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-08 20:29:44.765][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-08 20:29:44.767][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-08 20:29:44.768][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-08 20:29:44.769][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-08 20:29:44.771][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-08 20:29:44.772][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-08 20:29:44.773][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-08 20:29:44.775][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-08 20:29:44.776][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-08 20:29:44.777][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-08 20:29:44.779][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-08-08 20:29:44.780][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-08 20:29:44.781][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:44.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:44.783][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:44.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:44.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:44.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:44.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:44.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:44.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:44.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:44.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.971][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.DEBUG[2025-08-08 20:29:44.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:44.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:44.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:44.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:44.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.976][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.DEBUG[2025-08-08 20:29:44.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:44.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:44.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:44.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:44.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:44.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:44.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:44.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:44.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:44.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:44.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:44.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:44.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:44.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:44.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:44.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:44.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:44.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:44.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:44.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.000][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[2025-08-08 20:29:45.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.005][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[2025-08-08 20:29:45.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.011][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[2025-08-08 20:29:45.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.023][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.DEBUG[2025-08-08 20:29:45.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.028][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[2025-08-08 20:29:45.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.034][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[2025-08-08 20:29:45.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.040][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[2025-08-08 20:29:45.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.046][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[2025-08-08 20:29:45.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.052][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[2025-08-08 20:29:45.053][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-08 20:29:45.055][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-08 20:29:45.057][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:45.058][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-08 20:29:45.059][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:45.060][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-08 20:29:45.061][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:45.061][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-08 20:29:45.062][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:45.063][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-08 20:29:45.064][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-08 20:29:45.065][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-08 20:29:45.066][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:45.067][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-08 20:29:45.068][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-08 20:29:45.069][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-08 20:29:45.069][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-08 20:29:45.069][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-08 20:29:45.069][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-08 20:29:45.069][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-08 20:29:45.069][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-08 20:29:45.069][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-08 20:29:45.069][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-08 20:29:45.069][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-08 20:29:45.069][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-08 20:29:45.069][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-08 20:29:45.070][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:45.071][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-08 20:29:45.071][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-08 20:29:45.071][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-08 20:29:45.072][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-08 20:29:45.073][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:45.074][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:45.075][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-08 20:29:45.076][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:45.077][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:45.077][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-08 20:29:45.078][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-08 20:29:45.078][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-08 20:29:45.079][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-08 20:29:45.080][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-08 20:29:45.081][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:45.082][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-08 20:29:45.082][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-08 20:29:45.083][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-08 20:29:45.085][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-08 20:29:45.087][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-08 20:29:45.088][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-08 20:29:45.089][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-08 20:29:45.091][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-08 20:29:45.094][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-08 20:29:45.098][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-08 20:29:45.099][biodb::testThat]
biodb.INFO [2025-08-08 20:29:45.100][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2025-08-08 20:29:45.101][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-08 20:29:45.102][biodb::testThat]
sched.DEBUG[2025-08-08 20:29:45.105][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
fscache.INFO [2025-08-08 20:29:45.107][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:45.113][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/a2ed8f44d213d85be0d7e9a0448c78ad.content.
sched.DEBUG[2025-08-08 20:29:45.114][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
sched.DEBUG[2025-08-08 20:29:45.118][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 [2025-08-08 20:29:45.121][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:45.123][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/a18c63ccef4470d3f0d2883a74f87ee1.content.
sched.DEBUG[2025-08-08 20:29:45.124][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:45.126][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:45.127][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.133][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.135][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-08-08 20:29:45.138][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 [2025-08-08 20:29:45.141][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:45.143][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/b6b884df7b7bd565d1ac86525427e09b.content.
sched.DEBUG[2025-08-08 20:29:45.144][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:45.146][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:45.147][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.153][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.155][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.177][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:45.178][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.184][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.187][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.188][FUN] Functions in observer 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[2025-08-08 20:29:45.193][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 [2025-08-08 20:29:45.196][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:45.198][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/a18c63ccef4470d3f0d2883a74f87ee1.content.
sched.DEBUG[2025-08-08 20:29:45.199][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:45.201][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:45.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.211][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.212][FUN] Functions in observer 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[2025-08-08 20:29:45.214][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 [2025-08-08 20:29:45.217][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:45.219][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/b6b884df7b7bd565d1ac86525427e09b.content.
sched.DEBUG[2025-08-08 20:29:45.221][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:45.222][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:45.223][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.230][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.232][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.234][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:45.235][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.241][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-08-08 20:29:45.248][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 [2025-08-08 20:29:45.251][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:45.253][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/a18c63ccef4470d3f0d2883a74f87ee1.content.
sched.DEBUG[2025-08-08 20:29:45.254][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:45.261][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:45.262][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.269][FUN] Functions in observer 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[2025-08-08 20:29:45.271][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 [2025-08-08 20:29:45.274][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:45.276][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/b6b884df7b7bd565d1ac86525427e09b.content.
sched.DEBUG[2025-08-08 20:29:45.277][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:45.278][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:45.279][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.284][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.286][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.286][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".
sched.DEBUG[2025-08-08 20:29:45.288][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 [2025-08-08 20:29:45.290][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:45.293][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/d853ab8a48594978d76c30b86726648a.content.
sched.DEBUG[2025-08-08 20:29:45.293][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:45.295][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:45.296][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.301][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.303][FUN] Functions in observer BiodbConfig: [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 [2025-08-08 20:29:45.309][biodb::testThat]
biodb.INFO [2025-08-08 20:29:45.310][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2025-08-08 20:29:45.311][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-08 20:29:45.312][biodb::testThat]
sched.DEBUG[2025-08-08 20:29:45.314][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 [2025-08-08 20:29:45.317][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:45.319][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/aa56e28005d49da17591454624aabcd2.content.
sched.DEBUG[2025-08-08 20:29:45.320][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:45.321][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:45.322][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.327][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.328][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-08-08 20:29:45.333][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 [2025-08-08 20:29:45.335][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:45.337][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/c62078a064e3122e21e26c3428179396.content.
sched.DEBUG[2025-08-08 20:29:45.338][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:45.339][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:45.340][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.345][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.347][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.347][FUN] Functions in observer BiodbConfig: [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 [2025-08-08 20:29:45.351][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-08-08 20:29:45.353][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-08 20:29:45.353][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-08 20:29:45.354][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.356][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.357][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-08 20:29:45.361][biodb::testContext]
biodb.INFO [2025-08-08 20:29:45.362][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-08 20:29:45.363][biodb::testContext] Test context - Test web services
biodb.INFO [2025-08-08 20:29:45.364][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-08 20:29:45.365][biodb::testContext]
biodb.INFO [2025-08-08 20:29:45.367][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-08-08 20:29:45.368][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-08-08 20:29:45.372][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-08 20:29:45.373][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-08 20:29:45.374][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-08 20:29:45.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.377][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-08 20:29:45.378][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-08 20:29:45.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.382][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-08 20:29:45.383][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-08 20:29:45.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.386][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-08 20:29:45.387][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-08 20:29:45.388][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-08 20:29:45.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.391][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-08 20:29:45.392][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-08 20:29:45.393][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-08 20:29:45.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.397][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-08 20:29:45.398][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-08 20:29:45.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.401][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-08 20:29:45.402][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-08 20:29:45.403][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-08 20:29:45.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.406][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-08 20:29:45.407][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-08 20:29:45.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.411][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-08 20:29:45.412][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-08 20:29:45.413][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-08 20:29:45.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.416][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-08 20:29:45.417][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-08 20:29:45.418][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-08 20:29:45.419][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-08 20:29:45.420][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-08 20:29:45.421][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-08 20:29:45.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.425][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-08 20:29:45.426][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-08 20:29:45.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.430][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-08 20:29:45.431][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-08 20:29:45.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.433][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.DEBUG[2025-08-08 20:29:45.434][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-08 20:29:45.435][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-08 20:29:45.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.439][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-08 20:29:45.440][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-08 20:29:45.441][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-08 20:29:45.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.444][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-08 20:29:45.445][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-08 20:29:45.449][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-08 20:29:45.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.453][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-08 20:29:45.454][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-08 20:29:45.455][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-08 20:29:45.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.458][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-08 20:29:45.460][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:45.461][self$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[2025-08-08 20:29:45.462][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:45.463][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-08 20:29:45.464][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:45.465][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-08 20:29:45.466][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:45.467][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-08 20:29:45.468][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-08 20:29:45.469][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-08 20:29:45.470][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:45.471][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-08 20:29:45.472][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-08 20:29:45.473][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:45.474][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:45.475][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-08 20:29:45.475][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-08 20:29:45.475][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-08 20:29:45.475][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-08 20:29:45.475][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-08 20:29:45.476][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-08 20:29:45.477][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:45.478][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:45.478][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-08 20:29:45.479][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:45.480][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:45.481][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-08 20:29:45.482][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:45.483][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-08 20:29:45.484][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-08 20:29:45.485][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:45.486][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:45.487][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-08 20:29:45.489][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:45.490][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-08 20:29:45.490][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:45.491][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-08 20:29:45.492][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:45.493][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-08 20:29:45.494][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:45.495][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-08 20:29:45.496][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-08 20:29:45.497][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-08 20:29:45.498][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:45.499][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-08 20:29:45.500][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-08 20:29:45.501][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:45.502][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:45.503][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-08 20:29:45.503][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-08 20:29:45.503][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-08 20:29:45.503][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-08 20:29:45.503][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-08 20:29:45.504][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-08 20:29:45.505][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:45.506][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:45.506][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-08 20:29:45.507][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:45.508][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:45.509][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-08 20:29:45.510][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:45.511][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-08 20:29:45.512][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-08 20:29:45.513][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:45.514][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:45.515][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-08 20:29:45.517][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:45.518][self$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[2025-08-08 20:29:45.518][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:45.519][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-08 20:29:45.520][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:45.521][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-08 20:29:45.522][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:45.523][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-08 20:29:45.524][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-08 20:29:45.525][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-08 20:29:45.526][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:45.527][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-08 20:29:45.528][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-08 20:29:45.529][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:45.530][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:45.531][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:45.537][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-08 20:29:45.537][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:45.538][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:45.539][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-08 20:29:45.540][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:45.541][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:45.542][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-08 20:29:45.543][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:45.544][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-08 20:29:45.544][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-08 20:29:45.545][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:45.546][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:45.547][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-08 20:29:45.549][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:45.550][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-08 20:29:45.551][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:45.552][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-08 20:29:45.553][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:45.554][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-08 20:29:45.555][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:45.556][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-08 20:29:45.557][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-08 20:29:45.558][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-08 20:29:45.558][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:45.559][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-08 20:29:45.560][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-08 20:29:45.561][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:45.562][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:45.563][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:45.564][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-08 20:29:45.565][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:45.566][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:45.567][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-08 20:29:45.568][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:45.569][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:45.569][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-08 20:29:45.570][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:45.571][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-08 20:29:45.572][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-08 20:29:45.573][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:45.574][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:45.575][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-08 20:29:45.576][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.577][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.DEBUG[2025-08-08 20:29:45.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.590][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[2025-08-08 20:29:45.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.594][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[2025-08-08 20:29:45.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.602][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[2025-08-08 20:29:45.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.611][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.DEBUG[2025-08-08 20:29:45.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.636][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.DEBUG[2025-08-08 20:29:45.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.640][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[2025-08-08 20:29:45.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.645][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-08 20:29:45.646][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-08 20:29:45.648][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-08 20:29:45.649][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-08 20:29:45.650][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-08 20:29:45.652][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-08 20:29:45.653][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-08 20:29:45.654][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-08 20:29:45.656][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-08 20:29:45.657][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-08 20:29:45.658][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-08 20:29:45.660][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-08 20:29:45.661][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-08 20:29:45.662][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-08 20:29:45.664][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-08 20:29:45.665][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-08 20:29:45.667][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-08 20:29:45.668][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-08 20:29:45.669][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-08 20:29:45.671][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-08 20:29:45.672][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-08 20:29:45.673][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-08 20:29:45.675][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-08 20:29:45.676][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-08 20:29:45.678][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-08 20:29:45.679][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-08 20:29:45.681][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-08 20:29:45.682][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-08 20:29:45.683][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-08 20:29:45.685][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-08 20:29:45.686][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-08 20:29:45.687][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-08 20:29:45.689][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-08 20:29:45.690][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-08 20:29:45.691][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-08 20:29:45.693][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-08 20:29:45.694][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-08 20:29:45.695][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-08 20:29:45.697][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-08 20:29:45.698][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-08 20:29:45.699][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-08 20:29:45.701][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-08 20:29:45.702][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-08 20:29:45.703][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-08 20:29:45.705][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-08 20:29:45.706][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-08 20:29:45.708][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-08 20:29:45.709][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-08 20:29:45.710][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-08 20:29:45.712][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-08 20:29:45.713][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-08 20:29:45.714][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-08 20:29:45.716][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-08 20:29:45.717][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-08 20:29:45.718][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-08 20:29:45.720][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-08 20:29:45.721][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-08 20:29:45.722][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-08 20:29:45.724][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-08 20:29:45.725][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-08 20:29:45.726][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-08 20:29:45.727][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-08 20:29:45.729][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-08 20:29:45.730][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-08 20:29:45.731][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-08 20:29:45.733][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-08 20:29:45.734][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-08 20:29:45.735][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-08 20:29:45.737][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-08 20:29:45.738][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-08 20:29:45.739][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-08 20:29:45.741][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-08 20:29:45.742][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-08 20:29:45.743][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-08 20:29:45.745][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-08 20:29:45.746][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-08 20:29:45.747][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-08 20:29:45.749][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-08 20:29:45.750][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-08 20:29:45.751][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-08 20:29:45.753][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-08 20:29:45.754][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-08 20:29:45.755][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-08 20:29:45.757][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-08 20:29:45.758][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-08-08 20:29:45.759][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-08 20:29:45.760][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.762][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.797][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[2025-08-08 20:29:45.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.832][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[2025-08-08 20:29:45.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.844][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[2025-08-08 20:29:45.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.861][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[2025-08-08 20:29:45.863][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-08 20:29:45.864][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-08 20:29:45.866][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:45.867][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-08 20:29:45.868][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:45.869][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-08 20:29:45.870][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:45.871][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-08 20:29:45.871][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:45.872][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-08 20:29:45.873][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-08 20:29:45.874][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-08 20:29:45.875][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:45.876][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-08 20:29:45.877][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-08 20:29:45.878][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-08 20:29:45.878][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-08 20:29:45.878][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-08 20:29:45.878][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-08 20:29:45.878][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-08 20:29:45.878][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-08 20:29:45.878][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-08 20:29:45.878][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-08 20:29:45.878][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-08 20:29:45.878][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-08 20:29:45.878][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-08 20:29:45.879][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:45.880][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-08 20:29:45.880][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-08 20:29:45.880][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-08 20:29:45.881][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-08 20:29:45.882][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:45.883][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:45.884][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-08 20:29:45.885][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:45.885][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:45.886][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-08 20:29:45.887][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-08 20:29:45.887][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-08 20:29:45.888][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-08 20:29:45.889][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-08 20:29:45.890][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:45.891][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-08 20:29:45.891][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-08 20:29:45.892][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-08 20:29:45.894][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-08 20:29:45.895][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-08 20:29:45.897][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-08 20:29:45.898][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-08 20:29:45.900][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-08 20:29:45.903][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-08 20:29:45.906][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-08 20:29:45.907][biodb::testThat]
biodb.INFO [2025-08-08 20:29:45.908][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-08-08 20:29:45.909][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-08 20:29:45.910][biodb::testThat]
sched.DEBUG[2025-08-08 20:29:45.912][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
fscache.INFO [2025-08-08 20:29:45.914][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:45.920][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/a2ed8f44d213d85be0d7e9a0448c78ad.content.
sched.DEBUG[2025-08-08 20:29:45.921][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
sched.DEBUG[2025-08-08 20:29:45.925][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
fscache.INFO [2025-08-08 20:29:45.927][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:45.929][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/45b8073beb9f4a9f751edf98e80ca9dd.content.
sched.DEBUG[2025-08-08 20:29:45.930][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.INFO [2025-08-08 20:29:45.937][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-08-08 20:29:45.939][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-08 20:29:45.939][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-08 20:29:45.940][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:45.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:45.942][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:45.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:45.944][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-08 20:29:45.948][biodb::testContext]
biodb.INFO [2025-08-08 20:29:45.949][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-08 20:29:45.950][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-08-08 20:29:45.950][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-08 20:29:45.951][biodb::testContext]
biodb.INFO [2025-08-08 20:29:45.953][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1.
biodb.DEBUG[2025-08-08 20:29:45.955][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-08-08 20:29:45.959][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-08 20:29:45.960][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-08 20:29:45.961][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-08 20:29:45.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.963][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[2025-08-08 20:29:45.964][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-08 20:29:45.965][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-08 20:29:45.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.968][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-08 20:29:45.969][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-08 20:29:45.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.972][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.DEBUG[2025-08-08 20:29:45.973][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-08 20:29:45.974][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-08 20:29:45.975][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-08 20:29:45.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.978][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-08 20:29:45.979][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-08 20:29:45.980][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-08 20:29:45.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.984][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-08 20:29:45.985][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-08 20:29:45.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.988][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-08 20:29:45.989][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-08 20:29:45.990][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-08 20:29:45.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.993][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[2025-08-08 20:29:45.994][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-08 20:29:45.995][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-08 20:29:45.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:45.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:45.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:45.998][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-08 20:29:45.999][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-08 20:29:46.000][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-08 20:29:46.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.003][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[2025-08-08 20:29:46.004][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-08 20:29:46.005][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-08 20:29:46.005][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-08 20:29:46.006][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-08 20:29:46.007][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-08 20:29:46.008][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-08 20:29:46.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:46.012][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-08 20:29:46.013][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-08 20:29:46.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.015][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[2025-08-08 20:29:46.016][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-08 20:29:46.017][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-08 20:29:46.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:46.021][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-08 20:29:46.022][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-08 20:29:46.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:46.025][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-08 20:29:46.026][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-08 20:29:46.027][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-08 20:29:46.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:46.031][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-08 20:29:46.032][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-08 20:29:46.035][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-08 20:29:46.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.038][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[2025-08-08 20:29:46.039][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-08 20:29:46.039][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-08 20:29:46.040][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-08 20:29:46.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:46.044][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-08 20:29:46.046][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:46.047][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-08 20:29:46.048][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:46.049][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-08 20:29:46.050][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:46.051][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-08 20:29:46.052][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:46.053][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-08 20:29:46.054][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-08 20:29:46.055][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-08 20:29:46.056][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:46.056][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-08 20:29:46.057][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-08 20:29:46.058][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:46.059][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:46.060][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-08 20:29:46.060][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-08 20:29:46.060][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-08 20:29:46.060][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-08 20:29:46.060][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-08 20:29:46.061][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-08 20:29:46.062][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:46.063][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:46.064][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-08 20:29:46.065][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:46.066][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:46.067][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-08 20:29:46.072][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:46.073][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-08 20:29:46.074][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-08 20:29:46.075][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:46.076][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:46.077][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-08 20:29:46.079][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:46.080][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-08 20:29:46.081][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:46.082][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-08 20:29:46.083][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:46.083][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-08 20:29:46.084][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:46.085][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-08 20:29:46.086][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-08 20:29:46.087][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-08 20:29:46.088][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:46.089][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-08 20:29:46.090][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-08 20:29:46.091][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:46.092][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:46.093][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-08 20:29:46.093][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-08 20:29:46.093][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-08 20:29:46.093][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-08 20:29:46.093][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-08 20:29:46.094][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-08 20:29:46.095][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:46.096][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:46.097][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-08 20:29:46.098][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:46.098][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:46.099][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-08 20:29:46.100][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:46.101][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-08 20:29:46.102][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-08 20:29:46.103][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:46.104][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:46.105][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-08 20:29:46.107][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:46.108][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-08 20:29:46.109][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:46.109][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-08 20:29:46.110][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:46.111][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-08 20:29:46.112][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:46.113][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-08 20:29:46.114][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-08 20:29:46.115][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-08 20:29:46.116][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:46.117][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-08 20:29:46.118][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-08 20:29:46.119][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:46.120][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:46.121][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:46.122][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-08 20:29:46.123][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:46.124][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:46.124][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-08 20:29:46.125][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:46.126][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:46.127][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-08 20:29:46.128][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:46.129][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-08 20:29:46.130][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-08 20:29:46.131][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:46.132][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:46.133][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-08 20:29:46.134][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:46.135][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-08 20:29:46.136][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:46.137][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-08 20:29:46.138][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:46.139][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-08 20:29:46.140][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:46.141][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-08 20:29:46.142][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-08 20:29:46.143][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-08 20:29:46.144][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:46.145][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-08 20:29:46.146][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-08 20:29:46.147][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:46.147][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:46.148][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:46.149][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-08 20:29:46.150][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:46.151][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:46.152][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-08 20:29:46.153][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:46.154][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:46.155][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-08 20:29:46.156][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:46.157][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-08 20:29:46.157][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-08 20:29:46.158][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:46.159][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-08 20:29:46.160][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-08 20:29:46.161][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:46.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:46.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:46.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.175][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".
biodb.DEBUG[2025-08-08 20:29:46.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:46.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:46.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:46.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:46.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.196][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[2025-08-08 20:29:46.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.201][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[2025-08-08 20:29:46.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.205][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[2025-08-08 20:29:46.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.209][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[2025-08-08 20:29:46.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:46.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.218][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[2025-08-08 20:29:46.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.222][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[2025-08-08 20:29:46.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.226][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[2025-08-08 20:29:46.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.231][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.DEBUG[2025-08-08 20:29:46.232][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-08 20:29:46.233][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-08 20:29:46.235][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-08 20:29:46.236][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-08 20:29:46.237][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-08 20:29:46.239][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-08 20:29:46.240][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-08 20:29:46.241][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-08 20:29:46.243][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-08 20:29:46.244][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-08 20:29:46.245][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-08 20:29:46.247][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-08 20:29:46.248][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-08 20:29:46.249][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-08 20:29:46.251][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-08 20:29:46.252][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-08 20:29:46.253][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-08 20:29:46.255][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-08 20:29:46.256][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-08 20:29:46.257][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-08 20:29:46.259][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-08 20:29:46.260][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-08 20:29:46.261][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-08 20:29:46.263][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-08 20:29:46.264][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-08 20:29:46.265][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-08 20:29:46.267][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-08 20:29:46.268][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-08 20:29:46.269][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-08 20:29:46.271][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-08 20:29:46.272][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-08 20:29:46.273][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-08 20:29:46.275][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-08 20:29:46.276][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-08 20:29:46.277][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-08 20:29:46.279][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-08 20:29:46.280][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-08 20:29:46.281][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-08 20:29:46.283][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-08 20:29:46.284][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-08 20:29:46.285][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-08 20:29:46.287][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-08 20:29:46.288][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-08 20:29:46.289][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-08 20:29:46.291][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-08 20:29:46.292][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-08 20:29:46.293][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-08 20:29:46.295][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-08 20:29:46.296][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-08 20:29:46.297][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-08 20:29:46.299][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-08 20:29:46.300][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-08 20:29:46.301][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-08 20:29:46.303][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-08 20:29:46.304][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-08 20:29:46.305][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-08 20:29:46.306][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-08 20:29:46.308][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-08 20:29:46.309][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-08 20:29:46.310][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-08 20:29:46.312][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-08 20:29:46.313][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-08 20:29:46.314][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-08 20:29:46.316][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-08 20:29:46.317][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-08 20:29:46.318][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-08 20:29:46.320][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-08 20:29:46.321][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-08 20:29:46.322][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-08 20:29:46.324][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-08 20:29:46.325][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-08 20:29:46.331][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-08 20:29:46.333][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-08 20:29:46.334][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-08 20:29:46.335][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-08 20:29:46.336][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-08 20:29:46.338][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-08 20:29:46.339][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-08 20:29:46.340][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-08 20:29:46.342][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-08 20:29:46.343][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-08 20:29:46.344][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-08 20:29:46.346][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-08 20:29:46.347][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-08 20:29:46.348][initialize] This is biodb version 1.17.1.
biodb.DEBUG[2025-08-08 20:29:46.349][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-08 20:29:46.350][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.352][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:46.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:46.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:46.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:46.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:46.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:46.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:46.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:46.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:46.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:46.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:46.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:46.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:46.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:46.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:46.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:46.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:46.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:46.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:46.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:46.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:46.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.394][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.DEBUG[2025-08-08 20:29:46.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:46.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:46.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:46.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:46.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:46.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.405][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[2025-08-08 20:29:46.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:46.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:46.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.411][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[2025-08-08 20:29:46.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:46.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:46.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.417][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[2025-08-08 20:29:46.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:46.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:46.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.423][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[2025-08-08 20:29:46.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:46.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:46.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.429][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[2025-08-08 20:29:46.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:46.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:46.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:46.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:46.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:46.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:46.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-08 20:29:46.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:46.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:46.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-08 20:29:46.449][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-08 20:29:46.450][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-08 20:29:46.452][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:46.453][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-08 20:29:46.454][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:46.455][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-08 20:29:46.456][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:46.457][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-08 20:29:46.458][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:46.459][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-08 20:29:46.460][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-08 20:29:46.461][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-08 20:29:46.462][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:46.463][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-08 20:29:46.464][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-08 20:29:46.465][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-08 20:29:46.465][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-08 20:29:46.465][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-08 20:29:46.465][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-08 20:29:46.465][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-08 20:29:46.465][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-08 20:29:46.465][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-08 20:29:46.465][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-08 20:29:46.465][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-08 20:29:46.465][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-08 20:29:46.465][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-08 20:29:46.466][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-08 20:29:46.467][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-08 20:29:46.467][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-08 20:29:46.467][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-08 20:29:46.468][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-08 20:29:46.469][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:46.469][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:46.470][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-08 20:29:46.471][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-08 20:29:46.472][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-08 20:29:46.473][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-08 20:29:46.474][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-08 20:29:46.474][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-08 20:29:46.475][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-08 20:29:46.476][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-08 20:29:46.477][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-08 20:29:46.478][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-08 20:29:46.478][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-08 20:29:46.479][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-08 20:29:46.481][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-08 20:29:46.482][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-08 20:29:46.483][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-08 20:29:46.485][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-08 20:29:46.486][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-08 20:29:46.490][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-08 20:29:46.493][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-08 20:29:46.494][biodb::testThat]
biodb.INFO [2025-08-08 20:29:46.495][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-08-08 20:29:46.496][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-08 20:29:46.497][biodb::testThat]
sched.DEBUG[2025-08-08 20:29:46.499][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
fscache.INFO [2025-08-08 20:29:46.501][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:46.507][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/a2ed8f44d213d85be0d7e9a0448c78ad.content.
sched.DEBUG[2025-08-08 20:29:46.508][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
sched.DEBUG[2025-08-08 20:29:46.511][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 [2025-08-08 20:29:46.514][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
fscache.DEBUG[2025-08-08 20:29:46.516][FUN] Found encoding ISO-8859-1 for file /home/biocbuild/.cache/R/sched/45b8073beb9f4a9f751edf98e80ca9dd.content.
sched.DEBUG[2025-08-08 20:29:46.517][self$getBiodb()$getRequestScheduler( ...] Content loaded from cache.
biodb.DEBUG[2025-08-08 20:29:46.520][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-08-08 20:29:46.523][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
fscache.INFO [2025-08-08 20:29:46.524][cch$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
fscache.DEBUG[2025-08-08 20:29:46.533][FUN] Found encoding UTF-8 for file /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml.
biodb.DEBUG[2025-08-08 20:29:46.535][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-08 20:29:46.536][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-08 20:29:46.537][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-08 20:29:46.538][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-08 20:29:46.539][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:46.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:46.544][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.546][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-08 20:29:46.550][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:46.551][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:46.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.553][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:46.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:46.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.558][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:46.559][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:46.560][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.561][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.563][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-08 20:29:46.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-08 20:29:46.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.566][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:46.567][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:46.568][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.569][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.571][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-08 20:29:46.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-08 20:29:46.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.574][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-08 20:29:46.575][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-08 20:29:46.576][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.577][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.579][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-08 20:29:46.580][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-08 20:29:46.580][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.581][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.583][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:46.584][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:46.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.586][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.587][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:46.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-08 20:29:46.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.591][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:46.592][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:46.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.594][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.595][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-08 20:29:46.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-08 20:29:46.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.599][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:46.600][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:46.601][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.602][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:46.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-08 20:29:46.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.607][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:46.612][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:46.613][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.614][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.616][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-08 20:29:46.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-08 20:29:46.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.620][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:46.621][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:46.622][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.623][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.624][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-08 20:29:46.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-08 20:29:46.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.628][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:46.629][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:46.629][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.630][ef$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.632][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-08 20:29:46.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-08 20:29:46.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:46.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:46.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:46.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:46.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:46.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:46.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-08 20:29:46.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-08 20:29:46.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:46.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:46.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:46.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:46.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:46.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:46.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:46.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:46.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:46.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:46.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-08 20:29:46.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-08 20:29:46.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-08 20:29:46.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-08 20:29:46.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-08 20:29:46.672][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-08-08 20:29:46.675][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-08-08 20:29:46.676][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-08 20:29:46.677][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-08 20:29:46.678][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-08 20:29:46.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-08 20:29:46.680][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-08 20:29:46.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-08 20:29:46.681][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-08 20:29:46.682][FUN] Functions in observer 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 
 14.902   0.457  17.046

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn0.6770.0620.742
ChebiEntry0.1470.0120.158