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This page was generated on 2025-09-01 11:39 -0400 (Mon, 01 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4606
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4547
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 206/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-08-28 13:40 -0400 (Thu, 28 Aug 2025)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: RELEASE_3_21
git_last_commit: b8d718f
git_last_commit_date: 2025-04-15 12:39:10 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for biodbChebi on merida1

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: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.14.0.tar.gz
StartedAt: 2025-08-29 00:32:19 -0400 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 00:35:27 -0400 (Fri, 29 Aug 2025)
EllapsedTime: 188.2 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbChebi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/biodbChebi.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
ChebiConn 4.48  1.237  12.829
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

biodbChebi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbChebi
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘biodbChebi’ ...
** this is package ‘biodbChebi’ version ‘1.14.0’
** 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 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 [2025-08-29 00:34:01.972][biodb::testContext]
biodb.INFO [2025-08-29 00:34:01.979][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-29 00:34:01.981][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-08-29 00:34:01.983][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-29 00:34:01.985][biodb::testContext]
biodb.INFO [2025-08-29 00:34:01.998][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-08-29 00:34:02.001][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-29 00:34:02.014][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 00:34:02.017][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-29 00:34:02.019][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-29 00:34:02.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:02.027][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-29 00:34:02.075][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-29 00:34:02.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:02.084][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-29 00:34:02.086][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-29 00:34:02.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:02.095][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-29 00:34:02.097][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-29 00:34:02.100][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-29 00:34:02.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:02.108][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-29 00:34:02.110][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-29 00:34:02.113][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-29 00:34:02.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:02.122][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-29 00:34:02.124][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-29 00:34:02.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.131][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.DEBUG[2025-08-29 00:34:02.133][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-29 00:34:02.135][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-29 00:34:02.138][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-29 00:34:02.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:02.146][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-29 00:34:02.149][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-29 00:34:02.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.156][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[2025-08-29 00:34:02.158][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-29 00:34:02.160][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-29 00:34:02.163][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-29 00:34:02.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:02.171][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-29 00:34:02.174][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-29 00:34:02.177][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-29 00:34:02.179][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-29 00:34:02.182][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-29 00:34:02.185][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-29 00:34:02.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:02.193][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-29 00:34:02.196][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-29 00:34:02.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:02.204][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-29 00:34:02.207][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-29 00:34:02.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:02.215][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-29 00:34:02.218][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-29 00:34:02.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:02.226][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-29 00:34:02.229][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-29 00:34:02.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:02.237][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-29 00:34:02.240][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-29 00:34:02.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:02.249][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-29 00:34:02.251][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-29 00:34:02.269][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-29 00:34:02.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:02.278][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-29 00:34:02.281][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-29 00:34:02.283][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-29 00:34:02.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:02.297][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-29 00:34:02.379][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 00:34:02.429][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-29 00:34:02.432][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 00:34:02.434][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 00:34:02.437][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 00:34:02.439][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 00:34:02.442][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 00:34:02.444][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 00:34:02.446][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-29 00:34:02.449][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 00:34:02.452][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 00:34:02.454][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-29 00:34:02.456][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 00:34:02.459][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 00:34:02.461][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 00:34:02.463][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 00:34:02.463][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 00:34:02.463][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 00:34:02.463][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-29 00:34:02.463][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-29 00:34:02.466][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 00:34:02.468][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:34:02.470][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:34:02.473][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 00:34:02.475][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:34:02.477][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:34:02.479][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 00:34:02.481][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 00:34:02.483][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 00:34:02.484][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 00:34:02.486][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 00:34:02.489][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 00:34:02.492][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-29 00:34:02.496][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 00:34:02.499][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-29 00:34:02.501][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 00:34:02.503][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 00:34:02.505][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 00:34:02.508][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 00:34:02.510][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 00:34:02.512][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 00:34:02.515][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-29 00:34:02.517][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 00:34:02.519][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 00:34:02.521][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-29 00:34:02.523][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 00:34:02.526][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 00:34:02.528][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 00:34:02.531][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 00:34:02.531][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 00:34:02.531][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 00:34:02.531][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-29 00:34:02.531][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-29 00:34:02.533][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 00:34:02.536][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:34:02.538][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:34:02.541][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 00:34:02.543][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:34:02.546][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:34:02.548][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 00:34:02.550][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 00:34:02.553][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 00:34:02.555][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 00:34:02.557][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 00:34:02.559][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 00:34:02.562][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-29 00:34:02.566][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-29 00:34:02.569][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-29 00:34:02.571][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 00:34:02.573][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 00:34:02.576][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 00:34:02.578][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 00:34:02.581][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 00:34:02.583][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 00:34:02.586][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-29 00:34:02.588][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 00:34:02.591][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-29 00:34:02.594][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-29 00:34:02.596][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 00:34:02.599][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 00:34:02.602][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 00:34:02.604][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-29 00:34:02.607][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 00:34:02.609][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:34:02.612][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:34:02.615][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 00:34:02.617][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:34:02.619][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:34:02.622][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 00:34:02.624][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 00:34:02.626][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 00:34:02.628][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 00:34:02.631][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 00:34:02.633][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 00:34:02.635][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-29 00:34:02.639][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-29 00:34:02.642][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-29 00:34:02.644][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 00:34:02.646][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 00:34:02.648][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 00:34:02.651][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 00:34:02.653][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 00:34:02.672][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 00:34:02.675][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-29 00:34:02.677][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 00:34:02.679][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-29 00:34:02.682][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-29 00:34:02.684][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 00:34:02.686][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 00:34:02.688][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 00:34:02.691][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-29 00:34:02.694][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 00:34:02.696][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:34:02.699][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:34:02.701][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 00:34:02.704][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:34:02.706][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:34:02.708][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 00:34:02.710][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 00:34:02.713][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 00:34:02.715][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 00:34:02.717][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 00:34:02.719][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 00:34:02.727][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 00:34:02.729][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:02.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:02.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:02.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.774][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[2025-08-29 00:34:02.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:02.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:02.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:02.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:02.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:02.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:02.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:02.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:02.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:02.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:02.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:02.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:02.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:02.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:02.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:02.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:02.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:02.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:02.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:02.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:02.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.931][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.DEBUG[2025-08-29 00:34:02.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:02.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:02.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:02.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:02.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:02.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:02.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:02.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:02.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.968][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[2025-08-29 00:34:02.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:02.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:02.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.977][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[2025-08-29 00:34:02.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:02.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:02.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:02.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:02.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:02.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:02.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:02.997][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[2025-08-29 00:34:02.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:03.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:03.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:03.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:03.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:03.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:03.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:03.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:03.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:03.017][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[2025-08-29 00:34:03.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:03.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:03.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:03.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:03.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:03.028][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-29 00:34:03.037][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-29 00:34:03.040][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-29 00:34:03.044][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-29 00:34:03.047][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-29 00:34:03.051][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-29 00:34:03.054][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-29 00:34:03.058][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-29 00:34:03.061][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-29 00:34:03.065][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-29 00:34:03.069][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-29 00:34:03.072][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-29 00:34:03.076][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-29 00:34:03.080][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-29 00:34:03.083][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-29 00:34:03.087][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-29 00:34:03.090][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-29 00:34:03.094][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-29 00:34:03.098][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-29 00:34:03.101][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-29 00:34:03.104][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-29 00:34:03.108][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-29 00:34:03.111][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-29 00:34:03.115][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-29 00:34:03.119][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-29 00:34:03.122][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-29 00:34:03.126][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-29 00:34:03.129][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-29 00:34:03.133][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-29 00:34:03.136][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-29 00:34:03.140][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-29 00:34:03.143][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-29 00:34:03.147][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-29 00:34:03.150][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-29 00:34:03.154][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-29 00:34:03.157][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-29 00:34:03.161][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-29 00:34:03.165][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-29 00:34:03.168][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-29 00:34:03.172][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-29 00:34:03.175][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-29 00:34:03.179][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-29 00:34:03.183][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-29 00:34:03.186][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-29 00:34:03.190][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-29 00:34:03.193][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-29 00:34:03.196][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-29 00:34:03.200][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-29 00:34:03.204][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-29 00:34:03.207][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-29 00:34:03.210][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-29 00:34:03.214][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-29 00:34:03.217][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-29 00:34:03.221][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-29 00:34:03.224][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-29 00:34:03.228][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-29 00:34:03.231][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-29 00:34:03.235][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-29 00:34:03.238][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-29 00:34:03.242][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-29 00:34:03.246][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-29 00:34:03.249][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-29 00:34:03.253][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-29 00:34:03.257][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-29 00:34:03.260][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-29 00:34:03.264][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-29 00:34:03.267][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-29 00:34:03.271][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-29 00:34:03.275][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-29 00:34:03.278][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-29 00:34:03.281][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-29 00:34:03.286][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-29 00:34:03.289][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-29 00:34:03.293][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-29 00:34:03.296][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-29 00:34:03.300][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-29 00:34:03.303][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-29 00:34:03.307][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-29 00:34:03.310][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-29 00:34:03.314][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-29 00:34:03.317][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-29 00:34:03.321][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-29 00:34:03.324][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-29 00:34:03.338][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-29 00:34:03.342][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-08-29 00:34:03.349][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 00:34:03.351][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:03.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:03.356][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:03.358][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.DEBUG[2025-08-29 00:34:03.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:03.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:03.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:03.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:03.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:03.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:03.392][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[2025-08-29 00:34:03.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:03.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:03.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:03.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:03.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:03.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:03.406][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[2025-08-29 00:34:03.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:03.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:03.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:03.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:03.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:03.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:03.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:03.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:03.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:03.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:03.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:03.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:03.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:03.431][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[2025-08-29 00:34:03.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:03.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:03.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:03.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:03.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:03.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:03.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:03.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:03.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:03.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:03.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:03.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:03.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:03.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:03.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:03.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:03.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:03.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:03.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:03.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:03.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:03.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:03.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:03.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:03.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:03.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:03.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:03.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:03.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:03.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:03.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:03.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:03.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:03.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:03.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:03.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:03.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:03.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:03.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:03.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:03.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:03.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:03.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:03.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:03.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:03.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:03.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:03.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:03.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:03.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:03.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:03.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:03.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:03.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:03.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:03.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:03.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:03.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:03.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:03.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:03.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:03.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:03.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:03.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:03.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:03.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:03.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:03.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:03.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:03.576][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[2025-08-29 00:34:03.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:03.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:03.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:03.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:03.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:03.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:03.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:03.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:03.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:03.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:03.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:03.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:03.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:03.598][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[2025-08-29 00:34:03.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:34:03.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:03.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:03.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:03.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:03.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:03.611][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[2025-08-29 00:34:03.615][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-29 00:34:03.640][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-29 00:34:03.644][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 00:34:03.647][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-29 00:34:03.650][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 00:34:03.652][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 00:34:03.655][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 00:34:03.657][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 00:34:03.659][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-29 00:34:03.662][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-29 00:34:03.664][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-29 00:34:03.666][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 00:34:03.668][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 00:34:03.670][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-29 00:34:03.673][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 00:34:03.675][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-29 00:34:03.675][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-29 00:34:03.675][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-29 00:34:03.675][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-29 00:34:03.675][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-29 00:34:03.675][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-29 00:34:03.675][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-29 00:34:03.675][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-29 00:34:03.675][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-29 00:34:03.675][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-29 00:34:03.675][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-29 00:34:03.678][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-29 00:34:03.681][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 00:34:03.681][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 00:34:03.681][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 00:34:03.683][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-29 00:34:03.685][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:34:03.688][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:34:03.690][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 00:34:03.692][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:34:03.694][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:34:03.696][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 00:34:03.698][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:34:03.698][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-29 00:34:03.701][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 00:34:03.703][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 00:34:03.705][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-29 00:34:03.708][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-29 00:34:03.708][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-29 00:34:03.722][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-29 00:34:03.726][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-29 00:34:03.729][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-29 00:34:03.733][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-29 00:34:03.736][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-29 00:34:03.740][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-29 00:34:03.813][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-29 00:34:03.815][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-08-29 00:34:03.823][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-08-29 00:34:03.830][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-08-29 00:34:03.838][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-29 00:34:03.840][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-29 00:34:03.843][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-08-29 00:34:03.846][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-29 00:34:03.862][biodb::testThat]
biodb.INFO [2025-08-29 00:34:03.865][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-08-29 00:34:03.867][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 00:34:03.869][biodb::testThat]
biodb.TRACE[2025-08-29 00:34:03.876][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-08-29 00:34:03.880][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:34:03.887][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:34:03.902][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:03.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:03.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:03.933][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:03.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:03.937][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:03.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:03.955][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:03.958][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:03.960][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:03.962][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:03.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:03.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:04.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.006][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:04.008][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:04.010][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.012][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.083][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:04.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:04.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.092][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:04.095][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:04.097][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.099][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.102][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:04.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:04.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.112][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:04.115][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:04.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.119][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.123][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:04.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:04.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.134][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:04.136][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:04.139][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.141][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.143][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:04.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:04.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.153][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:04.155][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:04.157][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.159][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.162][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:04.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:04.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.170][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:04.172][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:04.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.177][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.180][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:04.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:04.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.189][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:04.191][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:04.193][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.195][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.210][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:04.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:04.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.220][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:04.223][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:04.225][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.226][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.228][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:04.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:04.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.237][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:04.239][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:04.242][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.244][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.247][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:04.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:04.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.256][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:04.259][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:04.261][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.263][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.266][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:04.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:04.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.275][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:04.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:04.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.284][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:04.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:04.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:04.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:04.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.303][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:04.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:04.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:04.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:04.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:04.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:04.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:04.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:04.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:04.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:04.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:04.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:04.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:04.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:04.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:04.453][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-08-29 00:34:04.459][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:04.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:04.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.469][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:04.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:04.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.547][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:04.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:04.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.556][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:04.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:04.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.565][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:04.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:04.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:04.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:04.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.583][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-29 00:34:04.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-29 00:34:04.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.592][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-29 00:34:04.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-29 00:34:04.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.601][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-29 00:34:04.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-29 00:34:04.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.609][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-29 00:34:04.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-29 00:34:04.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:04.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:04.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.752][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:04.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:04.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:04.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:04.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:04.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:04.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:04.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:04.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:04.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:04.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:04.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:04.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:04.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:04.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.836][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:04.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:04.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.845][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:04.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:04.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.855][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:04.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:04.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:04.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:04.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:04.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:04.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:04.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:04.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.952][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:04.955][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:04.957][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.959][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:04.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:04.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:04.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:04.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:05.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:05.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:05.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:05.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:05.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:05.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.028][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:05.031][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:05.033][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.036][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.038][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:05.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:05.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.064][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:05.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:05.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.073][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:05.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:05.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.082][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:05.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:05.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.092][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:05.094][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:05.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.098][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.101][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:05.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:05.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.128][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:05.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:05.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.139][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:05.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:05.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.148][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:05.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:05.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.158][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:05.160][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:05.162][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.164][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.167][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:05.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:05.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.196][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:05.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:05.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.206][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:05.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:05.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:05.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:05.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.225][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:05.228][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:05.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.233][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:05.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:05.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:05.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:05.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:05.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:05.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:05.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:05.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.292][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:05.295][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:05.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.299][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:05.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:05.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.329][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:05.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:05.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.347][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:05.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:05.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.357][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:05.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:05.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.365][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:05.367][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:05.369][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.371][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.373][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:05.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:05.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.400][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-29 00:34:05.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:05.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.409][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-29 00:34:05.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:05.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.418][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-29 00:34:05.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:05.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.427][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-29 00:34:05.429][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:05.432][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.434][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.436][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-29 00:34:05.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:05.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.464][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:05.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:05.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.474][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:05.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:05.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.484][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:05.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:05.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.494][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:05.497][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:05.499][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.502][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.504][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:05.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:05.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.530][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:05.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:05.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.540][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:05.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:05.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.550][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:05.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:05.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.560][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:05.563][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:05.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.568][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.570][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:05.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:05.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.596][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:05.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:05.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.606][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:05.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:05.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.616][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:05.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:05.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.625][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:05.627][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:05.629][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.632][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.633][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:05.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:05.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.659][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:05.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:05.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.669][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:05.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:05.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.679][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:05.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:05.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.697][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:05.700][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:05.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.704][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.707][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:05.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:05.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.736][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:05.739][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:05.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.744][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.755][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:05.758][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:05.760][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.762][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.774][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:05.777][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:05.779][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.782][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.793][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:05.796][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:05.798][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.801][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.812][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:05.815][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:05.817][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.820][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.831][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:05.833][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:05.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.838][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.850][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:05.852][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:05.855][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.857][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.867][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:05.869][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:05.870][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.872][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.883][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-29 00:34:05.886][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:05.888][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.890][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.902][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:05.905][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:05.907][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.909][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:05.920][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:05.923][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:05.925][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:05.928][ef$get] fields variable is a list.
biodb.INFO [2025-08-29 00:34:05.947][biodb::testThat]
biodb.INFO [2025-08-29 00:34:05.949][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-08-29 00:34:05.952][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 00:34:05.954][biodb::testThat]
biodb.DEBUG[2025-08-29 00:34:05.990][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-08-29 00:34:06.003][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 00:34:06.012][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-08-29 00:34:06.014][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 00:34:06.018][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-08-29 00:34:06.020][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:34:06.094][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:34:06.096][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:34:06.100][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:06.103][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:06.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:06.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:06.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:06.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:06.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:06.127][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:06.129][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:06.132][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.134][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:06.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:06.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.189][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:06.192][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:06.195][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.197][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.200][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:06.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:06.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.211][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:06.213][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:06.216][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.218][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.221][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:06.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:06.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.232][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:06.235][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:06.237][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.239][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.242][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:06.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:06.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.251][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:06.254][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:06.256][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.258][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.261][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:06.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:06.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.271][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:06.274][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:06.276][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.278][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.281][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:06.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:06.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.291][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:06.294][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:06.296][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.299][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.301][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:06.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:06.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.312][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:06.315][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:06.317][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.320][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.323][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:06.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:06.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.334][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:06.337][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:06.340][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.343][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.346][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:06.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:06.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.357][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:06.359][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:06.361][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.363][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.366][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:06.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:06.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.382][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:06.385][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:06.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.389][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.392][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:06.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:06.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.402][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:06.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:06.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:06.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:06.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:06.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:06.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.432][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:06.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:06.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:06.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:06.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:06.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:06.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:06.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:06.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:06.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:06.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:06.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:06.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:06.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:06.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:06.501][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-08-29 00:34:06.503][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-08-29 00:34:06.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-08-29 00:34:06.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-08-29 00:34:06.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-08-29 00:34:06.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-08-29 00:34:06.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-08-29 00:34:06.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-29 00:34:06.553][biodb::testThat]
biodb.INFO [2025-08-29 00:34:06.556][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-08-29 00:34:06.559][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 00:34:06.561][biodb::testThat]
biodb.TRACE[2025-08-29 00:34:06.568][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:06.571][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:06.573][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.575][ef$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:06.578][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-08-29 00:34:06.642][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:06.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:06.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.651][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:06.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:06.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:06.662][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:06.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:06.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:06.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:06.682][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-08-29 00:34:06.691][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-08-29 00:34:06.752][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 00:34:06.794][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-08-29 00:34:06.796][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 00:34:06.799][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-08-29 00:34:06.860][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:34:06.869][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:06.871][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:06.875][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-08-29 00:34:07.609][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-08-29 00:34:08.072][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:08.077][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-08-29 00:34:08.155][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-08-29 00:34:08.161][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-08-29 00:34:08.190][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:08.192][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:08.194][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:08.195][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:08.198][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:08.200][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:08.203][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:08.205][ef$get] fields variable is a list.
biodb.INFO [2025-08-29 00:34:08.215][biodb::testThat]
biodb.INFO [2025-08-29 00:34:08.217][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-08-29 00:34:08.219][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 00:34:08.221][biodb::testThat]
biodb.TRACE[2025-08-29 00:34:08.295][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:08.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:08.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:08.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:08.304][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:08.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:08.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:08.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:08.313][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:08.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:08.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:08.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:08.458][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:34:08.466][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 00:34:08.469][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-29 00:34:08.472][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 00:34:08.475][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-08-29 00:34:08.520][biodb::testThat]
biodb.INFO [2025-08-29 00:34:08.522][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-08-29 00:34:08.524][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 00:34:08.527][biodb::testThat]
biodb.TRACE[2025-08-29 00:34:08.575][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:08.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:08.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:08.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:08.585][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:08.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:08.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:08.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:08.595][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:08.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:08.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:08.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:08.605][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:08.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:08.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:08.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:08.615][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:08.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:08.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:08.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:08.625][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:08.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:08.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:08.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:08.635][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-29 00:34:08.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-29 00:34:08.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:08.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:08.646][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-29 00:34:08.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-29 00:34:08.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:08.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:08.657][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-29 00:34:08.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-29 00:34:08.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:08.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:08.667][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-29 00:34:08.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-29 00:34:08.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:08.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:08.724][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:08.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:08.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:08.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:08.732][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:08.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:08.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:08.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:08.743][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:08.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:08.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:08.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:08.752][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:08.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:08.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:08.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:08.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:08.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:08.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:08.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:08.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:08.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:08.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:08.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:08.789][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-29 00:34:08.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-29 00:34:08.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:08.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:08.799][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-29 00:34:08.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-29 00:34:08.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:08.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:08.808][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-29 00:34:08.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-29 00:34:08.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:08.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:08.818][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-29 00:34:08.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-29 00:34:08.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:08.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-29 00:34:08.840][biodb::testThat]
biodb.INFO [2025-08-29 00:34:08.842][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-08-29 00:34:08.845][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 00:34:08.846][biodb::testThat]
biodb.INFO [2025-08-29 00:34:08.864][biodb::testThat]
biodb.INFO [2025-08-29 00:34:08.867][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-08-29 00:34:08.869][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 00:34:08.872][biodb::testThat]
biodb.INFO [2025-08-29 00:34:08.893][biodb::testThat]
biodb.INFO [2025-08-29 00:34:08.895][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-08-29 00:34:08.898][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 00:34:08.900][biodb::testThat]
biodb.DEBUG[2025-08-29 00:34:08.908][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-08-29 00:34:09.441][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-08-29 00:34:10.197][biodb::testThat]
biodb.INFO [2025-08-29 00:34:10.199][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-08-29 00:34:10.201][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 00:34:10.204][biodb::testThat]
biodb.DEBUG[2025-08-29 00:34:10.608][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2025-08-29 00:34:11.014][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:11.016][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:11.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:11.020][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:11.022][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:11.025][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:11.027][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:11.029][ef$get] fields variable is a list.
biodb.INFO [2025-08-29 00:34:11.033][biodb::testThat]
biodb.INFO [2025-08-29 00:34:11.035][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-08-29 00:34:11.038][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 00:34:11.040][biodb::testThat]
biodb.TRACE[2025-08-29 00:34:11.064][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:11.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:11.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:11.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:11.091][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:11.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:11.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:11.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:11.099][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:11.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:11.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:11.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:11.274][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:34:11.282][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 00:34:11.285][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-29 00:34:11.288][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 00:34:11.292][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-08-29 00:34:11.456][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:34:11.464][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 00:34:11.467][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-29 00:34:11.471][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 00:34:11.473][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-08-29 00:34:11.505][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-29 00:34:11.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-29 00:34:11.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:11.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:11.525][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:11.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:11.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:11.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:11.534][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:11.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:11.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:11.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:11.543][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:11.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:11.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:11.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:11.560][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:11.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:11.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:11.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:11.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:11.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:11.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:11.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:11.590][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:34:11.633][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:11.636][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:11.679][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-08-29 00:34:12.069][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-08-29 00:34:12.459][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:12.464][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-08-29 00:34:12.474][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-08-29 00:34:12.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:12.482][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:12.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:12.496][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:12.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:12.500][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:12.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:12.506][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-08-29 00:34:12.649][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 00:34:12.653][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-08-29 00:34:12.656][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 00:34:12.658][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 00:34:12.660][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:34:12.663][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:34:12.666][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 00:34:12.668][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 00:34:12.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:12.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:12.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:12.689][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:12.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:12.693][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:12.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:12.698][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-08-29 00:34:12.705][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:12.707][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:12.710][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-08-29 00:34:13.222][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-08-29 00:34:13.608][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:13.626][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-08-29 00:34:13.674][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-08-29 00:34:13.686][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-08-29 00:34:13.697][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 00:34:13.700][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:34:13.703][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:34:13.707][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:13.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:13.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:13.735][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:13.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:13.740][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:13.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:13.760][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:13.762][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:13.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:13.767][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:13.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:13.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:13.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:13.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:13.779][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:13.782][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:13.784][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:13.786][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:13.789][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:13.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:13.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:13.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:13.799][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:13.801][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:13.804][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:13.806][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:13.810][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:13.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:13.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:13.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:13.819][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:13.822][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:13.825][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:13.827][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:13.830][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:13.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:13.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:13.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:13.839][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:13.841][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:13.843][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:13.845][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:13.847][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:13.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:13.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:13.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:13.855][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:13.857][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:13.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:13.861][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:13.863][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:13.865][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:13.867][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:13.869][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:13.871][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:13.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:13.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:13.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:13.880][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:13.883][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:13.885][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:13.888][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:13.890][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:13.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:13.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:13.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:13.900][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:13.902][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:13.904][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:13.906][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:13.910][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:13.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:13.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:13.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:13.920][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:13.923][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:13.925][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:13.927][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:13.930][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:13.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:13.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:13.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:13.939][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:13.942][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:13.944][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:13.946][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:13.949][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:13.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:13.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:13.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:13.959][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:13.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:13.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:13.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:13.968][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:13.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:13.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:13.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:13.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:13.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:13.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:13.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:13.995][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:13.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:14.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:14.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:14.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:14.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:14.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:14.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:14.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:14.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:14.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:14.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:14.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:14.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:14.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:14.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:14.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:14.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:14.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:14.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:14.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:14.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:14.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:14.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:14.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:14.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:14.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:14.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:14.059][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-08-29 00:34:14.084][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:14.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:14.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:14.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:14.093][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:14.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:14.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:14.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:14.102][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:14.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:14.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:14.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:14.113][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:34:14.121][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:14.124][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:14.128][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-08-29 00:34:14.515][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-08-29 00:34:14.898][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:14.903][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-08-29 00:34:14.923][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-08-29 00:34:14.979][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:14.981][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:14.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:14.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:14.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:15.000][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:15.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:15.004][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:15.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:15.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:15.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:15.013][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:15.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:15.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:15.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:15.022][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:15.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:15.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:15.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:15.032][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:15.034][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:15.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:15.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:15.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:15.052][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:15.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:15.056][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-08-29 00:34:15.059][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 00:34:15.063][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-08-29 00:34:15.066][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 00:34:15.068][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 00:34:15.071][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:34:15.074][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:34:15.076][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 00:34:15.079][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 00:34:15.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:15.117][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:15.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:15.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:15.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:15.136][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:15.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:15.141][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-08-29 00:34:15.148][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:15.151][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:15.154][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-08-29 00:34:15.559][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-08-29 00:34:15.947][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:15.952][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-08-29 00:34:15.999][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-08-29 00:34:16.006][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-08-29 00:34:16.010][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 00:34:16.013][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:34:16.016][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:34:16.020][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:16.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:16.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:16.049][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:16.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:16.054][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:16.056][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[2025-08-29 00:34:16.061][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:16.064][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:16.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.068][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:16.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:16.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.081][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:16.083][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:16.085][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.087][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.090][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:16.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:16.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.100][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:16.103][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:16.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.108][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.112][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:16.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:16.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.122][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:16.125][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:16.128][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.131][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.133][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:16.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:16.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.144][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:16.147][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:16.150][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.152][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.155][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:16.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:16.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.166][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:16.169][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:16.171][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.174][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.176][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:16.179][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:16.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.184][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.187][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:16.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:16.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.196][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:16.199][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:16.201][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.203][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.206][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:16.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:16.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.218][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:16.220][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:16.225][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.228][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.233][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:16.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:16.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.243][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:16.246][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:16.249][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.251][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.254][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:16.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:16.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.267][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:16.269][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:16.272][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.274][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.279][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:16.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:16.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.290][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:16.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:16.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:16.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:16.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:16.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:16.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.368][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:16.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:16.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:16.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:16.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:16.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:16.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:16.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:16.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:16.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:16.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:16.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:16.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:16.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:16.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:16.441][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-08-29 00:34:16.444][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:16.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:16.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.454][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:16.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:16.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.465][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:16.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:16.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:16.522][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:34:16.533][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 00:34:16.537][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-29 00:34:16.540][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 00:34:16.543][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-08-29 00:34:16.551][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:16.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:16.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:16.568][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:16.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:16.573][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:16.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:16.577][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:16.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:16.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.588][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:16.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:16.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:16.639][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:16.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:16.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:16.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:16.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:16.652][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:16.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:16.684][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:16.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:16.689][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:16.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:16.696][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-08-29 00:34:16.699][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 00:34:16.703][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-08-29 00:34:16.706][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 00:34:16.709][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 00:34:16.711][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:34:16.714][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:34:16.717][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 00:34:16.719][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 00:34:16.725][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:16.727][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:16.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:16.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:16.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:16.745][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:16.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:16.750][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-08-29 00:34:16.757][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:16.760][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:16.763][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-08-29 00:34:17.163][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-08-29 00:34:17.553][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:17.558][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-08-29 00:34:17.589][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-08-29 00:34:17.595][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-08-29 00:34:17.599][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 00:34:17.602][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:34:17.604][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:34:17.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:17.610][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:17.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:17.623][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:17.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:17.628][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:17.630][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[2025-08-29 00:34:17.636][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:17.638][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:17.641][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.643][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:17.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:17.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.656][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:17.659][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:17.661][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.663][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.666][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:17.669][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:17.671][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.673][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.677][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:17.679][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:17.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.684][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.687][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:17.689][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:17.692][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.693][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.696][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:17.698][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:17.701][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.703][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.719][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:17.722][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:17.725][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.727][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.730][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:17.732][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:17.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.736][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.739][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:17.741][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:17.744][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.746][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.749][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:17.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:17.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.758][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:17.760][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:17.762][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.764][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.767][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:17.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:17.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.776][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:17.778][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:17.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.783][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.785][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:17.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:17.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.795][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:17.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:17.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:17.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:17.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:17.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:17.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:17.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:17.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:17.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:17.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:17.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:17.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:17.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:17.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:17.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:17.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:17.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:17.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:17.874][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-08-29 00:34:17.876][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:17.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:17.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.886][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:17.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:17.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:17.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:17.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.904][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:17.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:17.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:17.914][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:17.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:17.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:17.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:17.925][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:17.927][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:17.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:17.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:17.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:17.952][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:17.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:17.957][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-08-29 00:34:17.959][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 00:34:17.962][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-08-29 00:34:17.965][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 00:34:17.968][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 00:34:17.970][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:34:17.972][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:34:17.975][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 00:34:17.977][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 00:34:17.983][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:17.985][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:17.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:17.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:18.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:18.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:18.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:18.008][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-08-29 00:34:18.014][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:18.017][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:18.020][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-08-29 00:34:18.430][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-08-29 00:34:18.816][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:18.821][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-08-29 00:34:18.864][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-08-29 00:34:18.870][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-08-29 00:34:18.874][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 00:34:18.877][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:34:18.879][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:34:18.883][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:18.885][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:18.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:18.897][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:18.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:18.902][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:18.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:18.909][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:18.911][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:18.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:18.916][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:18.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:18.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:18.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:18.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:18.927][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:18.930][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:18.932][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:18.934][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:18.936][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:18.939][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:18.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:18.944][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:18.947][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:18.950][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:18.952][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:18.954][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:18.957][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:18.960][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:18.962][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:18.965][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:18.968][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:18.971][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:18.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:18.976][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:18.979][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:18.981][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:18.984][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:18.986][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:18.989][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:18.992][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:18.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:18.997][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:19.013][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:19.016][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:19.019][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:19.021][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:19.025][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:19.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:19.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:19.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:19.036][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:19.039][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:19.041][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:19.044][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:19.047][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:19.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:19.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:19.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:19.056][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:19.059][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:19.061][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:19.063][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:19.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:19.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:19.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:19.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:19.077][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:19.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:19.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:19.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:19.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:19.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:19.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:19.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:19.097][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:19.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:19.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:19.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:19.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:19.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:19.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:19.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:19.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:19.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:19.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:19.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:19.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:19.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:19.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:19.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:19.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:19.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:19.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:19.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:19.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:19.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:19.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:19.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:19.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:19.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:19.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:19.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:19.165][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-08-29 00:34:19.168][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:19.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:19.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:19.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:19.176][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:19.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:19.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:19.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:19.185][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:19.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:19.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:19.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:19.195][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:19.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:19.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:19.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:19.204][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:19.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:19.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:19.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:19.213][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:19.215][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:19.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:19.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:19.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:19.233][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:19.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:19.238][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-08-29 00:34:19.241][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 00:34:19.253][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-08-29 00:34:19.256][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 00:34:19.259][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 00:34:19.262][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:34:19.264][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:34:19.267][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 00:34:19.269][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 00:34:19.275][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:19.277][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:19.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:19.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:19.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:19.295][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:19.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:19.300][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-08-29 00:34:19.306][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:19.308][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:19.312][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-08-29 00:34:19.712][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-08-29 00:34:20.099][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:20.104][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-08-29 00:34:20.112][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-08-29 00:34:20.118][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-08-29 00:34:20.122][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 00:34:20.125][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:34:20.127][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:34:20.130][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:20.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:20.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:20.145][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:20.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:20.149][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:20.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:20.156][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:20.159][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:20.161][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.163][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:20.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:20.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.175][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:20.178][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:20.180][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.182][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.185][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:20.187][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:20.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.191][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.195][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:20.197][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:20.200][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.202][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.205][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:20.207][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:20.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.212][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.215][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:20.218][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:20.220][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.222][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.225][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:20.228][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:20.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.232][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.234][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:20.237][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:20.239][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.242][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.244][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:20.247][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:20.249][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.251][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.256][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:20.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:20.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.276][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:20.277][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:20.278][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.280][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.281][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:20.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:20.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.287][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:20.289][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:20.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.293][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:20.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:20.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:20.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:20.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:20.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:20.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:20.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:20.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:20.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:20.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:20.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:20.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:20.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:20.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:20.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:20.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:20.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:20.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:20.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:20.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:20.390][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-08-29 00:34:20.392][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:20.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:20.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:20.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:20.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.410][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:20.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:20.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.419][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:20.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:20.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:20.429][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:20.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:20.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:20.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:20.440][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:20.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:20.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:20.455][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:20.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:20.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:20.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:20.463][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-08-29 00:34:20.466][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 00:34:20.469][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-08-29 00:34:20.472][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 00:34:20.475][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 00:34:20.477][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:34:20.479][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:34:20.481][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 00:34:20.491][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 00:34:20.495][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:20.497][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:20.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:20.507][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:20.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:20.511][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:20.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:20.516][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-08-29 00:34:20.522][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:20.525][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:20.528][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-08-29 00:34:20.947][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-08-29 00:34:21.343][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:21.347][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-08-29 00:34:21.355][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-08-29 00:34:21.362][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-08-29 00:34:21.365][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 00:34:21.368][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:34:21.371][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:34:21.374][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:21.376][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:21.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:21.389][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:21.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:21.393][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:21.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:21.400][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:21.402][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:21.405][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.407][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:21.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:21.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.419][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:21.421][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:21.422][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.423][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.425][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:21.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:21.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.434][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:21.436][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:21.439][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.441][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.443][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:21.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:21.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.452][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:21.454][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:21.457][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.459][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.462][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:21.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:21.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.471][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:21.473][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:21.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.478][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.480][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:21.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:21.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.489][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:21.492][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:21.494][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.496][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.499][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:21.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:21.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.508][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:21.524][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:21.526][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.528][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.531][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:21.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:21.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.541][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:21.544][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:21.546][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.549][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.551][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:21.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:21.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.561][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:21.563][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:21.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.567][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.571][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:21.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:21.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.580][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:21.582][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:21.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.587][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.591][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:21.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:21.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.601][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:21.604][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:21.606][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.608][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.611][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:21.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:21.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:21.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:21.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:21.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:21.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:21.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:21.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.659][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:21.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:21.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:21.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:21.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:21.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:21.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:21.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:21.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:21.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:21.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:21.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:21.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:21.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:21.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:21.725][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-08-29 00:34:21.728][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:21.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:21.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:21.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:21.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:21.748][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:21.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:21.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:21.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:21.767][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:21.769][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:21.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:21.783][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:21.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:21.788][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:21.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:21.793][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-08-29 00:34:21.797][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 00:34:21.801][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-08-29 00:34:21.804][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 00:34:21.807][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 00:34:21.809][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:34:21.812][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:34:21.814][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 00:34:21.817][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 00:34:21.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:21.825][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:21.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:21.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:21.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:21.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:21.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:21.845][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-08-29 00:34:21.851][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:21.854][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:21.857][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-08-29 00:34:22.267][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-08-29 00:34:22.655][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:22.659][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-08-29 00:34:22.667][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-08-29 00:34:22.674][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-08-29 00:34:22.678][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 00:34:22.681][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:34:22.684][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:34:22.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:22.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:22.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:22.704][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:22.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:22.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:22.711][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[2025-08-29 00:34:22.715][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:22.718][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:22.720][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:22.722][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:22.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:22.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:22.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:22.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:22.736][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:22.738][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:22.741][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:22.743][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:22.746][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:22.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:22.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:22.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:22.756][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:22.758][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:22.760][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:22.763][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:22.766][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:22.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:22.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:22.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:22.777][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:22.780][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:22.783][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:22.785][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:22.788][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:22.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:22.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:22.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:22.812][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:22.815][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:22.817][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:22.819][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:22.822][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:22.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:22.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:22.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:22.833][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:22.836][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:22.838][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:22.840][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:22.843][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:22.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:22.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:22.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:22.853][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:22.856][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:22.858][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:22.861][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:22.863][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:22.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:22.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:22.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:22.874][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:22.877][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:22.879][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:22.881][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:22.884][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:22.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:22.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:22.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:22.894][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:22.897][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:22.899][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:22.902][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:22.905][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:22.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:22.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:22.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:22.915][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:22.918][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:22.920][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:22.923][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:22.926][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:22.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:22.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:22.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:22.936][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:22.938][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:22.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:22.943][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:22.946][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:22.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:22.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:22.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:22.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:22.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:22.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:22.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:22.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:22.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:22.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:22.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:22.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:22.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:22.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:22.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:22.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:22.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:22.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:22.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:22.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:23.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:23.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:23.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:23.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:23.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:23.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:23.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:23.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:23.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:23.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:23.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:23.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:23.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:23.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:23.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:23.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:23.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:23.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:23.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:23.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:23.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:23.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:23.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:23.067][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-08-29 00:34:23.069][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:23.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:23.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:23.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:23.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:23.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:23.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:23.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:23.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:23.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:23.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:23.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:23.128][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:23.130][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:23.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:23.152][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:23.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:23.157][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:23.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:23.162][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-08-29 00:34:23.164][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 00:34:23.168][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-08-29 00:34:23.172][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 00:34:23.175][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 00:34:23.177][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:34:23.181][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:34:23.183][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 00:34:23.186][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 00:34:23.192][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:23.194][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:23.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:23.208][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:23.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:23.213][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:23.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:23.219][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-08-29 00:34:23.227][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:23.229][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:23.233][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-08-29 00:34:23.631][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-08-29 00:34:24.022][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:24.026][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-08-29 00:34:24.034][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-08-29 00:34:24.040][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-08-29 00:34:24.044][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 00:34:24.047][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:34:24.050][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:34:24.054][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:24.056][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:24.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:24.069][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:24.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:24.074][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:24.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:24.082][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:24.085][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:24.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.089][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:24.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:24.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.102][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:24.106][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:24.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.111][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.129][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:24.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:24.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.140][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:24.143][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:24.146][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.148][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.151][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:24.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:24.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.161][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:24.164][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:24.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.169][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.171][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:24.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:24.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.181][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:24.184][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:24.186][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.189][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.192][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:24.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:24.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.201][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:24.204][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:24.206][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.208][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.211][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:24.213][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:24.215][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.217][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.220][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:24.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:24.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.229][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:24.231][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:24.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.236][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:24.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:24.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.248][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:24.250][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:24.253][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.255][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.258][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:24.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:24.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.268][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:24.271][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:24.273][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.275][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.278][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:24.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:24.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.288][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:24.290][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:24.292][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.294][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.298][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:24.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:24.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:24.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:24.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:24.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:24.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:24.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:24.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.334][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:24.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:24.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:24.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:24.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:24.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:24.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:24.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:24.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:24.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:24.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:24.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:24.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:24.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:24.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:24.407][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-08-29 00:34:24.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:24.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:24.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.419][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:24.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:24.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:24.428][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:24.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:24.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:24.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:24.438][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:24.440][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:24.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:24.454][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:24.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:24.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:24.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:24.463][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-08-29 00:34:24.465][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 00:34:24.469][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-08-29 00:34:24.472][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 00:34:24.475][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 00:34:24.477][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:34:24.480][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:34:24.482][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 00:34:24.484][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 00:34:24.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:24.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:24.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:24.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:24.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:24.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:24.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:24.514][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-08-29 00:34:24.520][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:24.523][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:24.526][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-08-29 00:34:24.929][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-08-29 00:34:25.324][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:25.329][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-08-29 00:34:25.366][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-08-29 00:34:25.372][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-08-29 00:34:25.375][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 00:34:25.378][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:34:25.380][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:34:25.384][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:25.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:25.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:25.398][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:25.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:25.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:25.417][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[2025-08-29 00:34:25.422][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:25.424][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:25.426][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.429][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:25.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:25.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.440][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:25.442][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:25.444][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.446][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.449][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:25.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:25.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.458][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:25.461][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:25.463][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.465][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.467][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:25.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:25.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.475][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:25.478][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:25.479][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.481][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.484][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:25.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:25.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.493][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:25.496][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:25.499][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.501][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.504][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:25.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:25.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.513][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:25.516][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:25.518][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.520][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.523][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:25.526][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:25.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.530][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.533][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:25.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:25.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.542][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:25.545][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:25.547][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.549][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.552][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:25.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:25.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.562][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:25.564][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:25.566][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.568][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.572][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:25.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:25.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.581][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:25.584][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:25.586][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.588][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.591][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:25.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:25.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.601][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:25.603][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:25.605][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.608][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.610][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:25.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:25.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.620][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:25.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:25.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:25.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:25.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:25.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:25.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.657][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:25.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:25.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:25.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:25.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:25.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:25.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:25.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:25.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:25.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:25.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:25.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:25.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:25.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:25.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:25.721][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-08-29 00:34:25.723][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:25.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:25.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.731][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:25.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:25.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:25.739][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:25.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:25.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:25.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:25.747][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:25.749][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:25.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:25.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:25.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:25.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:25.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:25.771][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-08-29 00:34:25.772][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 00:34:25.776][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-08-29 00:34:25.778][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 00:34:25.781][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 00:34:25.784][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:34:25.786][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:34:25.789][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 00:34:25.791][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 00:34:25.796][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:25.799][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:25.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:25.811][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:25.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:25.816][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:25.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:25.821][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-08-29 00:34:25.828][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:25.830][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:25.833][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-08-29 00:34:26.231][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-08-29 00:34:26.617][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:26.621][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-08-29 00:34:26.642][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-08-29 00:34:26.649][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-08-29 00:34:26.653][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 00:34:26.656][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:34:26.658][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:34:26.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:26.665][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:26.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:26.678][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:26.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:26.682][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:26.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:26.690][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:26.693][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:26.695][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.697][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:26.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:26.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.710][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:26.712][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:26.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.716][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.719][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:26.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:26.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.728][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:26.731][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:26.733][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.735][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.738][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:26.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:26.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.748][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:26.750][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:26.753][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.755][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.758][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:26.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:26.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.768][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:26.770][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:26.772][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.774][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.777][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:26.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:26.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.786][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:26.788][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:26.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.792][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.794][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:26.797][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:26.799][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.801][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.803][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:26.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:26.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.813][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:26.815][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:26.818][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.820][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:26.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:26.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.832][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:26.835][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:26.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.839][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.842][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:26.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:26.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.852][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:26.855][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:26.857][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.867][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.870][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:26.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:26.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.879][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:26.882][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:26.884][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.886][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.888][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:26.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:26.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.898][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:26.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:26.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.907][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:26.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:26.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:26.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:26.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:26.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:26.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:26.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:26.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:26.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:26.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:26.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:26.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:26.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:26.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:26.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:26.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:26.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:26.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:26.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:27.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:27.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:27.004][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-08-29 00:34:27.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:27.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:27.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:27.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:27.018][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:27.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:27.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:27.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:27.028][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:27.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:27.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:27.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:27.037][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:27.039][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:27.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:27.052][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:27.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:27.056][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:27.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:27.061][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-08-29 00:34:27.063][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 00:34:27.067][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-08-29 00:34:27.069][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 00:34:27.072][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 00:34:27.074][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:34:27.077][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:34:27.079][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 00:34:27.081][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 00:34:27.087][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:27.089][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:27.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:27.109][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:27.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:27.139][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:27.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:27.145][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-08-29 00:34:27.151][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:27.154][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:27.157][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-08-29 00:34:27.554][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-08-29 00:34:27.940][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:27.944][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-08-29 00:34:27.952][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-08-29 00:34:27.958][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-08-29 00:34:27.962][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 00:34:27.965][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:34:27.967][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:34:27.970][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:27.972][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:27.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:27.984][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:27.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:27.988][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:27.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:27.996][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:27.999][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:28.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.005][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:28.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:28.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.016][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:28.019][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:28.022][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.024][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.026][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:28.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:28.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.032][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:28.034][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:28.035][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.037][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.040][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:28.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:28.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.050][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:28.052][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:28.054][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.057][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.059][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:28.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:28.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.069][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:28.071][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:28.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.076][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.079][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:28.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:28.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.089][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:28.091][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:28.093][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.094][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.096][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:28.098][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:28.099][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.100][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.102][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:28.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:28.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.112][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:28.115][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:28.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.133][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.136][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:28.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:28.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.146][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:28.148][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:28.150][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.153][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.155][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:28.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:28.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.165][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:28.167][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:28.169][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.172][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.174][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:28.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:28.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.184][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:28.187][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:28.188][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.190][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.193][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:28.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:28.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.203][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:28.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:28.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:28.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:28.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:28.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:28.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.231][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:28.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:28.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:28.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:28.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:28.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:28.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:28.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:28.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:28.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:28.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:28.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:28.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:28.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:28.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:28.302][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-08-29 00:34:28.305][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:28.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:28.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:28.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:28.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:28.325][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:28.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:28.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:28.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:28.335][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:28.336][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:28.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:28.349][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:28.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:28.353][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:28.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:28.366][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-08-29 00:34:28.369][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 00:34:28.373][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-08-29 00:34:28.376][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 00:34:28.379][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 00:34:28.382][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:34:28.384][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:34:28.386][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 00:34:28.388][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 00:34:28.394][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:28.396][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:28.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:28.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:28.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:28.414][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:28.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:28.419][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-08-29 00:34:28.426][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:28.428][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:28.431][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-08-29 00:34:28.935][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-08-29 00:34:29.325][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:29.329][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-08-29 00:34:29.338][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-08-29 00:34:29.344][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-08-29 00:34:29.347][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 00:34:29.350][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:34:29.352][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:34:29.355][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:29.357][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:29.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:29.371][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:29.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:29.375][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:29.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:29.382][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:29.384][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:29.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.389][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:29.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:29.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.401][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:29.404][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:29.406][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.408][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.411][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:29.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:29.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.421][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:29.423][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:29.425][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.428][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.430][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:29.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:29.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.440][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:29.443][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:29.446][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.448][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.451][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:29.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:29.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.461][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:29.464][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:29.466][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.467][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.470][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:29.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:29.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.497][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:29.500][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:29.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.504][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.507][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:29.509][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:29.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.514][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.516][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:29.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:29.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.526][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:29.527][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:29.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.530][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.533][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:29.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:29.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.542][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:29.545][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:29.547][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.549][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.553][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:29.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:29.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.563][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:29.566][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:29.568][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.570][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.573][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:29.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:29.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.583][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:29.586][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:29.588][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.590][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.593][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:29.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:29.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:29.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:29.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.614][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:29.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:29.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:29.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:29.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:29.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:29.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:29.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:29.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:29.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:29.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:29.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:29.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:29.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:29.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:29.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:29.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:29.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:29.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:29.701][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-08-29 00:34:29.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:29.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:29.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:29.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:29.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:29.733][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:29.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:29.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:29.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:29.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:29.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:29.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:29.761][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:29.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:29.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:29.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:29.771][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-08-29 00:34:29.774][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 00:34:29.778][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-08-29 00:34:29.781][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 00:34:29.784][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 00:34:29.787][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:34:29.790][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:34:29.793][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 00:34:29.796][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 00:34:29.802][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:29.804][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:29.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:29.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:29.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:29.821][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:29.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:29.826][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-08-29 00:34:29.832][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:29.834][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:29.837][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-08-29 00:34:30.225][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-08-29 00:34:30.612][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:30.617][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-08-29 00:34:30.628][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-08-29 00:34:30.637][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-08-29 00:34:30.642][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 00:34:30.646][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:34:30.649][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:34:30.654][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:30.656][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:30.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:30.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:30.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:30.677][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:30.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:30.685][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:30.688][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:30.690][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.693][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:30.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:30.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.708][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:30.710][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:30.713][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.715][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.718][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:30.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:30.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.727][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:30.730][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:30.732][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.735][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.739][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:30.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:30.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.766][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:30.769][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:30.773][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.775][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.778][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:30.781][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:30.784][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.786][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.789][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:30.792][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:30.794][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.796][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.800][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:30.803][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:30.806][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.808][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.811][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:30.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:30.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.823][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:30.826][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:30.830][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.832][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:30.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:30.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.850][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:30.853][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:30.858][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.860][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.863][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:30.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:30.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.875][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:30.879][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:30.882][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.884][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.887][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:30.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:30.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.898][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:30.900][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:30.903][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.905][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.908][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:30.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:30.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:30.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:30.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:30.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:30.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.938][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:30.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:30.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:30.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:30.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:30.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:30.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:30.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:30.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:30.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:30.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:30.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:30.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:30.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:30.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:31.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:31.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:31.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:31.008][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-08-29 00:34:31.011][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:31.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:31.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:31.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:31.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:31.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:31.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:31.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:31.042][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:31.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:31.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:31.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:31.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:31.054][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:31.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:31.068][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:31.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:31.073][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:31.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:31.079][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-08-29 00:34:31.082][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 00:34:31.085][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-08-29 00:34:31.088][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 00:34:31.091][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 00:34:31.094][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:34:31.096][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:34:31.099][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 00:34:31.101][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 00:34:31.107][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:31.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:31.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:31.124][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:31.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:31.129][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:31.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:31.134][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-08-29 00:34:31.142][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:31.144][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:31.148][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-08-29 00:34:31.536][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-08-29 00:34:31.923][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:31.927][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-08-29 00:34:31.935][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-08-29 00:34:31.941][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-08-29 00:34:31.945][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 00:34:31.948][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:34:31.951][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:34:31.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:31.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:31.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:31.970][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:31.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:31.974][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:31.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:31.981][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:31.983][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:31.986][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:31.988][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:31.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:31.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:31.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:31.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.001][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:32.004][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:32.006][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.009][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.012][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:32.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:32.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.022][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:32.025][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:32.027][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.029][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.032][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:32.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:32.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.057][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:32.060][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:32.062][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.064][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.067][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:32.070][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:32.072][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.074][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.076][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:32.078][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:32.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.083][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.086][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:32.089][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:32.091][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.093][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.097][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:32.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:32.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.107][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:32.110][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:32.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.115][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.118][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:32.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:32.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.127][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:32.129][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:32.132][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.134][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.138][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:32.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:32.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.148][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:32.150][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:32.152][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.154][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.157][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:32.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:32.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.167][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:32.170][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:32.172][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.174][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.177][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:32.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:32.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.186][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:32.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:32.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:32.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:32.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.206][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:32.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:32.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:32.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:32.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:32.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:32.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:32.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:32.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:32.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:32.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:32.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:32.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:32.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:32.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:32.286][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-08-29 00:34:32.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:32.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:32.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:32.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:32.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:32.308][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:32.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:32.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:32.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:32.317][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:32.319][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:32.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:32.331][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:32.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:32.335][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:32.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:32.340][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-08-29 00:34:32.343][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 00:34:32.346][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-08-29 00:34:32.349][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 00:34:32.352][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 00:34:32.354][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:34:32.356][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:34:32.359][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 00:34:32.361][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 00:34:32.367][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:32.369][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:32.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:32.382][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:32.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:32.388][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:32.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:32.393][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-08-29 00:34:32.400][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:32.402][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:32.405][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-08-29 00:34:32.813][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-08-29 00:34:33.211][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:33.216][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-08-29 00:34:33.224][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-08-29 00:34:33.230][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-08-29 00:34:33.234][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 00:34:33.237][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:34:33.240][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:34:33.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:33.246][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:33.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:33.260][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:33.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:33.264][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:33.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:33.272][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:33.275][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:33.277][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.279][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:33.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:33.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.292][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:33.295][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:33.297][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.299][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.302][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:33.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:33.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.313][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:33.316][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:33.332][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.335][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.338][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:33.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:33.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.349][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:33.351][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:33.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.356][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.359][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:33.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:33.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.368][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:33.371][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:33.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.375][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.378][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:33.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:33.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.389][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:33.391][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:33.393][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.396][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.399][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:33.401][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:33.404][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.407][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.410][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:33.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:33.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.420][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:33.423][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:33.425][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.427][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.430][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:33.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:33.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.443][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:33.446][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:33.449][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.452][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.455][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:33.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:33.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.465][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:33.467][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:33.469][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.471][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.474][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:33.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:33.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.484][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:33.487][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:33.489][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.492][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.496][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:33.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:33.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.506][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:33.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:33.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.516][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:33.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:33.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:33.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:33.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:33.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:33.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:33.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:33.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:33.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:33.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:33.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:33.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:33.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:33.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:33.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:33.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:33.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:33.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:33.623][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-08-29 00:34:33.626][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:33.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:33.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:33.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:33.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:33.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:33.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:33.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:33.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:33.655][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:33.658][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:33.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:33.672][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:33.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:33.677][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:33.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:33.682][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-08-29 00:34:33.685][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 00:34:33.689][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-08-29 00:34:33.692][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 00:34:33.695][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 00:34:33.698][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:34:33.700][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:34:33.703][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 00:34:33.705][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 00:34:33.709][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:33.710][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:33.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:33.723][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:33.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:33.727][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:33.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:33.733][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-08-29 00:34:33.740][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:33.742][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:33.746][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-08-29 00:34:34.141][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-08-29 00:34:34.530][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:34.534][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-08-29 00:34:34.542][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-08-29 00:34:34.586][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-08-29 00:34:34.590][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 00:34:34.595][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:34:34.597][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:34:34.601][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:34.603][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:34.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:34.617][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:34.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:34.622][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:34.625][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.TRACE[2025-08-29 00:34:34.631][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:34.634][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:34.651][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.654][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:34.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:34.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.668][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:34.671][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:34.673][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.676][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.679][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:34.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:34.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.689][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:34.691][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:34.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.696][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.700][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:34.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:34.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.711][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:34.714][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:34.716][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.719][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.721][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:34.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:34.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.731][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:34.733][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:34.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.737][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.740][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:34.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:34.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.750][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:34.753][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:34.755][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.758][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.760][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:34.763][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:34.766][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.768][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.771][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:34.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:34.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.782][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:34.785][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:34.787][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.789][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:34.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:34.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.802][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:34.805][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:34.807][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.809][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.813][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:34.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:34.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.821][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:34.824][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:34.826][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.828][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.830][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:34.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:34.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.840][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:34.843][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:34.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.847][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.850][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:34.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:34.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.859][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:34.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:34.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:34.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:34.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:34.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:34.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.908][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:34.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:34.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:34.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:34.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:34.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:34.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:34.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:34.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:34.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:34.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:34.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:34.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:34.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:34.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:34.977][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-08-29 00:34:34.979][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:34.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:34.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:34.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:34.990][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:34.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:34.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:35.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:35.004][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:35.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:35.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:35.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:35.016][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:35.018][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:35.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:35.032][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:35.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:35.037][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:35.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:35.042][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-08-29 00:34:35.045][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 00:34:35.049][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-08-29 00:34:35.052][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 00:34:35.055][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 00:34:35.057][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:34:35.060][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:34:35.063][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 00:34:35.065][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 00:34:35.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:35.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:35.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:35.087][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:35.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:35.091][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:35.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:35.097][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-08-29 00:34:35.103][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:35.106][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:35.109][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-08-29 00:34:35.503][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-08-29 00:34:35.894][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:35.899][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-08-29 00:34:35.919][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-08-29 00:34:35.926][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-08-29 00:34:35.945][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 00:34:35.948][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:34:35.951][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:34:35.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:35.958][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:35.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:35.971][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:35.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:35.976][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:35.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:35.983][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:35.986][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:35.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:35.991][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:35.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:35.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:35.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.005][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:36.008][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:36.010][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.013][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.016][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:36.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:36.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.027][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:36.030][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:36.032][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.034][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.037][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:36.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:36.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.046][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:36.049][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:36.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.054][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.056][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:36.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:36.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.066][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:36.068][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:36.070][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.072][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.075][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:36.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:36.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.084][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:36.086][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:36.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.091][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.093][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:36.096][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:36.099][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.101][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.104][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:36.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:36.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.115][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:36.117][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:36.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.122][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.125][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:36.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:36.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.134][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:36.135][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:36.136][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.137][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.139][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:36.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:36.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.145][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:36.147][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:36.149][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.151][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.153][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:36.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:36.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.171][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:36.173][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:36.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.178][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.181][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:36.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:36.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.191][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:36.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:36.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.201][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:36.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:36.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:36.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:36.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.221][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:36.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:36.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:36.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:36.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:36.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:36.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:36.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:36.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:36.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:36.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:36.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:36.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:36.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:36.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:36.290][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-08-29 00:34:36.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:36.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:36.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.303][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:36.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:36.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:36.313][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:36.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:36.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:36.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:36.323][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:36.325][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:36.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:36.339][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:36.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:36.344][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:36.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:36.348][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-08-29 00:34:36.350][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 00:34:36.354][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-08-29 00:34:36.357][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 00:34:36.360][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 00:34:36.362][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:34:36.364][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:34:36.366][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 00:34:36.369][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 00:34:36.375][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:36.377][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:36.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:36.391][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:36.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:36.395][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:36.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:36.408][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-08-29 00:34:36.414][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:36.417][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:36.420][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-08-29 00:34:36.816][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-08-29 00:34:37.209][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:37.214][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-08-29 00:34:37.256][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-08-29 00:34:37.262][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-08-29 00:34:37.266][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 00:34:37.269][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:34:37.272][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:34:37.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:37.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:37.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:37.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:37.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:37.295][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:37.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:37.302][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:37.307][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:37.309][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.311][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:37.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:37.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.326][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:37.328][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:37.331][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.333][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.336][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:37.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:37.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.346][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:37.348][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:37.350][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.353][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.356][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:37.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:37.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.365][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:37.368][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:37.370][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.373][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.375][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:37.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:37.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.384][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:37.386][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:37.387][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.389][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.392][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:37.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:37.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.400][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:37.402][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:37.405][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.407][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.410][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:37.412][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:37.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.417][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.420][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:37.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:37.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.432][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:37.434][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:37.437][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.439][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:37.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:37.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.466][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:37.468][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:37.471][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.473][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.475][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:37.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:37.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.484][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:37.487][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:37.489][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.491][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.494][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:37.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:37.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.503][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:37.506][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:37.508][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.510][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.513][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:37.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:37.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:37.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:37.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:37.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:37.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:37.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:37.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.551][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:37.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:37.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:37.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:37.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:37.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:37.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:37.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:37.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:37.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:37.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:37.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:37.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:37.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:37.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:37.616][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-08-29 00:34:37.619][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:37.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:37.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.628][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:37.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:37.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:37.638][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:37.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:37.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:37.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:37.646][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:37.648][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:37.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:37.662][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:37.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:37.666][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:37.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:37.670][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-08-29 00:34:37.672][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 00:34:37.684][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-08-29 00:34:37.687][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 00:34:37.690][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 00:34:37.693][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:34:37.695][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:34:37.698][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 00:34:37.700][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 00:34:37.706][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:37.708][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:37.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:37.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:37.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:37.725][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:37.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:37.730][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-08-29 00:34:37.737][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:37.739][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:37.743][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-08-29 00:34:38.145][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-08-29 00:34:38.541][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:38.546][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-08-29 00:34:38.593][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-08-29 00:34:38.600][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-08-29 00:34:38.604][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 00:34:38.606][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:34:38.609][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:34:38.613][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:38.615][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:38.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:38.628][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:38.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:38.632][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:38.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:38.639][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:38.641][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:38.644][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.646][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:38.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:38.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.658][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:38.661][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:38.663][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.666][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.669][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:38.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:38.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.679][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:38.682][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:38.684][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.686][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.689][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:38.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:38.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.699][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:38.702][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:38.704][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.706][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.708][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:38.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:38.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.716][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:38.718][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:38.719][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.720][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.722][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:38.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:38.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.731][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:38.748][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:38.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.753][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.756][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:38.759][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:38.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.764][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.767][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:38.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:38.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.777][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:38.780][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:38.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.784][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:38.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:38.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.797][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:38.799][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:38.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.804][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.807][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:38.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:38.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.817][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:38.820][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:38.822][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.825][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.827][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:38.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:38.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.836][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:38.837][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:38.839][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.840][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.842][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:38.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:38.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.848][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:38.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:38.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:38.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:38.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:38.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:38.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.864][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:38.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:38.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:38.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:38.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:38.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:38.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:38.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:38.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:38.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:38.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:38.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:38.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:38.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:38.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:38.922][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-08-29 00:34:38.925][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:38.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:38.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.935][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:38.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:38.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:38.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:38.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:38.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:38.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:38.964][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:38.966][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:38.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:38.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:38.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:38.983][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:38.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:38.989][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-08-29 00:34:38.991][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 00:34:38.994][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-08-29 00:34:38.997][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 00:34:38.999][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 00:34:39.002][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:34:39.004][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:34:39.005][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 00:34:39.007][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 00:34:39.013][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:39.015][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:39.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:39.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:39.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:39.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:39.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:39.035][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-08-29 00:34:39.041][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:39.044][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:39.047][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-08-29 00:34:39.458][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-08-29 00:34:39.842][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:39.846][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-08-29 00:34:39.870][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-08-29 00:34:39.877][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-08-29 00:34:39.881][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 00:34:39.884][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:34:39.887][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:34:39.891][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:39.893][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:39.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:39.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:39.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:39.910][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:39.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:39.917][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:39.919][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:39.921][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:39.923][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:39.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:39.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:39.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:39.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:39.936][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:39.939][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:39.942][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:39.944][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:39.947][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:39.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:39.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:39.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:39.957][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:39.960][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:39.962][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:39.964][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:39.967][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:39.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:39.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:39.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:39.991][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:39.994][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:39.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:39.999][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:40.002][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:40.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:40.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:40.013][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:40.016][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:40.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.020][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:40.023][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:40.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:40.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:40.035][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:40.038][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:40.040][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.042][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:40.045][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:40.048][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:40.050][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.053][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:40.057][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:40.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:40.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:40.069][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:40.072][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:40.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.076][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:40.079][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:40.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:40.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:40.089][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:40.091][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:40.093][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.096][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:40.100][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:40.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:40.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:40.110][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:40.112][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:40.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.115][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:40.117][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:40.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:40.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:40.123][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:40.124][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:40.125][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.127][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:40.128][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:40.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:40.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:40.134][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:40.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:40.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:40.139][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:40.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:40.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:40.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:40.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:40.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:40.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:40.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:40.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:40.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:40.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:40.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:40.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:40.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:40.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:40.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:40.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:40.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:40.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:40.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:40.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:40.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:40.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:40.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:40.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:40.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:40.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:40.239][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-08-29 00:34:40.242][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:40.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:40.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:40.253][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:40.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:40.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:40.265][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:40.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:40.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:40.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:40.278][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:40.280][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:40.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:40.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:40.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:40.296][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:40.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:40.300][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-08-29 00:34:40.302][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 00:34:40.305][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-08-29 00:34:40.307][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 00:34:40.309][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 00:34:40.311][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:34:40.313][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:34:40.316][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 00:34:40.318][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 00:34:40.324][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:40.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:40.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:40.341][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:40.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:40.348][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:40.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:40.353][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-08-29 00:34:40.359][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:40.363][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:40.366][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-08-29 00:34:40.776][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-08-29 00:34:41.158][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:41.163][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-08-29 00:34:41.171][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-08-29 00:34:41.177][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-08-29 00:34:41.181][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 00:34:41.184][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:34:41.187][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:34:41.191][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:41.193][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:41.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:41.206][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:41.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:41.211][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:41.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:41.219][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:41.222][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:41.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.226][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:41.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:41.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.253][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:41.255][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:41.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.259][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.262][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:41.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:41.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.272][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:41.274][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:41.277][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.279][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.282][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:41.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:41.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.291][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:41.294][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:41.296][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.298][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.301][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:41.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:41.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.310][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:41.312][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:41.315][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.317][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.320][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:41.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:41.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.330][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:41.332][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:41.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.337][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.339][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:41.342][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:41.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.347][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.350][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:41.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:41.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.364][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:41.366][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:41.368][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.370][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:41.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:41.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.389][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:41.392][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:41.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.397][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.400][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:41.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:41.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.412][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:41.414][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:41.417][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.420][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.423][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:41.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:41.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.435][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:41.438][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:41.441][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.444][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.447][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:41.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:41.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.459][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:41.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:41.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.470][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:41.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:41.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:41.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:41.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.501][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:41.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:41.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:41.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:41.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:41.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:41.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:41.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:41.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:41.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:41.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:41.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:41.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:41.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:41.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:41.573][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-08-29 00:34:41.575][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:41.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:41.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.585][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:41.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:41.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.594][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:41.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:41.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:41.650][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:34:41.659][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 00:34:41.662][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-29 00:34:41.665][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 00:34:41.668][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-08-29 00:34:41.675][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:41.677][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:41.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:41.713][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:41.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:41.718][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:41.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:41.722][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:41.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:41.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.733][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:41.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:41.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.743][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:41.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:41.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:41.937][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:41.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:41.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:41.951][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:41.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:41.953][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:41.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:41.957][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:41.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:41.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.964][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:41.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:41.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.972][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:41.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:41.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:41.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:41.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:41.990][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:41.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:41.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:41.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:42.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:42.002][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:42.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:42.016][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:42.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:42.021][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:42.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:42.026][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.045][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.054][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.064][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:42.073][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:42.075][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:42.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:42.089][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:42.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:42.093][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:42.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:42.098][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.107][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.117][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.126][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:42.145][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:42.147][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:42.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:42.160][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:42.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:42.164][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:42.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:42.169][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.179][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.188][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:42.197][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:42.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:42.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:42.215][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:42.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:42.220][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:42.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:42.225][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.246][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:42.257][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:42.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:42.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:42.275][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:42.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:42.280][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:42.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:42.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.295][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.306][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:42.317][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:42.320][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:42.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:42.335][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:42.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:42.340][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:42.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:42.346][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.357][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.370][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:42.383][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:42.387][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:42.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:42.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:42.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:42.411][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:42.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:42.417][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.430][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.445][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:42.456][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:42.458][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:42.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:42.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:42.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:42.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:42.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:42.488][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.501][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.512][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:42.529][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:42.532][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:42.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:42.548][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:42.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:42.553][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:42.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:42.561][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.576][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.587][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:42.601][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:42.603][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:42.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:42.618][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:42.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:42.625][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:42.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:42.630][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.658][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:42.669][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:42.671][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:42.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:42.692][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:42.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:42.698][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:42.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:42.703][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.739][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:42.751][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:42.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:42.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:42.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:42.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:42.776][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:42.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:42.781][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.792][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.802][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:42.810][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:42.812][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:42.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:42.826][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:42.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:42.832][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:42.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:42.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.850][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.862][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:42.874][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:42.877][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:42.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:42.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:42.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:42.899][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:42.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:42.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.918][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:42.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:42.969][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:42.971][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:42.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:42.984][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:42.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:42.988][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:42.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:42.992][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:42.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:42.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:43.000][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:43.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:43.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:43.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:43.009][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:43.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:43.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:43.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:43.019][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:43.021][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:43.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:43.031][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:43.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:43.036][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:43.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:43.040][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:43.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:43.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:43.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:43.053][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:43.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:43.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:43.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:43.062][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:43.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:43.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:43.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:43.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:43.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:43.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:43.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:43.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:43.090][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:43.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:43.095][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:43.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:43.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:43.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:43.104][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:43.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:43.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:43.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:43.113][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:43.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:43.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:43.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:43.124][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:43.126][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:43.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:43.139][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:43.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:43.145][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:43.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:43.150][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:43.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:43.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:43.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:43.160][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:43.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:43.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:43.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:43.171][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:43.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:43.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:43.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:43.219][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:43.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:43.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:43.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:43.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:43.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:43.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:43.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:43.234][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:43.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:43.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:43.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:43.240][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:43.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:43.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:43.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:43.245][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:43.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:43.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:43.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:43.310][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:34:43.318][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:43.322][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:43.326][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-08-29 00:34:43.714][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-08-29 00:34:44.099][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:44.104][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-08-29 00:34:44.114][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-08-29 00:34:44.122][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:34:44.130][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:44.132][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:44.137][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-08-29 00:34:44.522][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-08-29 00:34:44.907][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:44.912][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-08-29 00:34:44.920][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-08-29 00:34:44.926][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:44.928][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:44.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:44.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:44.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:44.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:44.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:44.950][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-08-29 00:34:44.952][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 00:34:44.956][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-08-29 00:34:44.958][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 00:34:44.961][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 00:34:44.963][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:34:44.966][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:34:44.968][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 00:34:44.970][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 00:34:44.976][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:44.978][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:44.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:44.991][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:44.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:44.995][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:44.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:45.000][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-08-29 00:34:45.006][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:45.008][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:45.011][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-08-29 00:34:45.411][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-08-29 00:34:45.806][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:45.811][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-08-29 00:34:45.847][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-08-29 00:34:45.853][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-08-29 00:34:45.857][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 00:34:45.860][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:34:45.862][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:34:45.866][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:45.868][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:45.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:45.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:45.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:45.885][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:45.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:45.893][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:45.895][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:45.898][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:45.900][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:45.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:45.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:45.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:45.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:45.912][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:45.914][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:45.916][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:45.918][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:45.921][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:45.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:45.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:45.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:45.930][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:45.933][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:45.935][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:45.937][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:45.940][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:45.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:45.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:45.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:45.950][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:45.952][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:45.955][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:45.957][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:45.960][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:45.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:45.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:45.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:45.969][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:45.971][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:45.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:45.976][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:45.978][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:45.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:45.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:45.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:45.988][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:45.991][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:45.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:45.996][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:45.999][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:46.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:46.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:46.008][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:46.011][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:46.013][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.015][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:46.018][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:46.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:46.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:46.027][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:46.030][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:46.032][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.034][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:46.037][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:46.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:46.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:46.047][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:46.048][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:46.050][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.052][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:46.056][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:46.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:46.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:46.066][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:46.068][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:46.069][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.071][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:46.074][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:46.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:46.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:46.084][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:46.086][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:46.089][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.091][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:46.094][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:46.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:46.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:46.104][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:46.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:46.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:46.138][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:46.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:46.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:46.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:46.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:46.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:46.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:46.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:46.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:46.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:46.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:46.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:46.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:46.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:46.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:46.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:46.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:46.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:46.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:46.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:46.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:46.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:46.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:46.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:46.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:46.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:46.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:46.226][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-08-29 00:34:46.229][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:46.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:46.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:46.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:46.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:46.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:46.249][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:46.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:46.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:46.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:46.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:46.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:46.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:46.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:46.278][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:46.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:46.282][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:46.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:46.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:46.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:46.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:46.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:46.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:46.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:46.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:46.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:46.307][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:46.308][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:46.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:46.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:46.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:46.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:46.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:46.329][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-08-29 00:34:46.331][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 00:34:46.334][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-08-29 00:34:46.337][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 00:34:46.340][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 00:34:46.342][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:34:46.345][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:34:46.348][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 00:34:46.350][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 00:34:46.356][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:46.357][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:46.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:46.369][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:46.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:46.374][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:46.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:46.378][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-08-29 00:34:46.384][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:46.386][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:46.389][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-08-29 00:34:46.782][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-08-29 00:34:47.185][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:47.189][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-08-29 00:34:47.197][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-08-29 00:34:47.204][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-08-29 00:34:47.207][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 00:34:47.210][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:34:47.213][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:34:47.216][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:47.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:47.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:47.231][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:47.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:47.236][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:47.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:47.242][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:47.244][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:47.246][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.248][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:47.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:47.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.259][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:47.262][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:47.264][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.266][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.269][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:47.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:47.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.279][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:47.282][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:47.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.286][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.289][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:47.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:47.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.299][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:47.302][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:47.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.307][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.309][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:47.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:47.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.319][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:47.321][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:47.323][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.326][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.328][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:47.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:47.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.337][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:47.340][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:47.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.344][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.347][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:47.349][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:47.351][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.353][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.355][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:47.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:47.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.364][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.367][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.369][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.371][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.383][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:47.386][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:47.388][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.390][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.393][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:47.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:47.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.402][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:47.405][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:47.407][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.409][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.412][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:47.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:47.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.422][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:47.424][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:47.426][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.428][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.431][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:47.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:47.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:47.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:47.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.450][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:47.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:47.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:47.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:47.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:47.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:47.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:47.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:47.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:47.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:47.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:47.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:47.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:47.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:47.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:47.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:47.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:47.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:47.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:47.535][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-08-29 00:34:47.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.557][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:47.606][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:34:47.614][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 00:34:47.617][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-29 00:34:47.619][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 00:34:47.622][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-08-29 00:34:47.629][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:47.631][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:47.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:47.644][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:47.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:47.648][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:47.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:47.653][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.663][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:47.684][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:47.686][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:47.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:47.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:47.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:47.705][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:47.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:47.710][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.747][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:47.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:47.774][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:47.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:47.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:47.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:47.794][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:47.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:47.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.807][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:47.841][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:47.843][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:47.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:47.856][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:47.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:47.859][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:47.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:47.864][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.873][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.882][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.891][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.900][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:47.908][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:47.910][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:47.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:47.923][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:47.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:47.927][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:47.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:47.931][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.940][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:47.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:47.961][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:47.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:47.975][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:47.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:47.979][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:47.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:47.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:47.993][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:47.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:47.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.002][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:48.011][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:48.012][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:48.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:48.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:48.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:48.029][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:48.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:48.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:48.061][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:48.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:48.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:48.076][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:48.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:48.080][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:48.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:48.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.102][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:48.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:48.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:48.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:48.122][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:48.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:48.125][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:48.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:48.130][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.149][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:48.158][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:48.159][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:48.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:48.170][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:48.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:48.174][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:48.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:48.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.187][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.195][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:48.203][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:48.205][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:48.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:48.217][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:48.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:48.222][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:48.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:48.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.236][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.245][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:48.255][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:48.257][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:48.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:48.270][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:48.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:48.274][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:48.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:48.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.290][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:48.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:48.312][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:48.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:48.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:48.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:48.330][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:48.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:48.335][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.345][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:48.364][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:48.366][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:48.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:48.380][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:48.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:48.384][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:48.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:48.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.399][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:48.419][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:48.422][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:48.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:48.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:48.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:48.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:48.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:48.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.453][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:48.471][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:48.473][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:48.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:48.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:48.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:48.490][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:48.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:48.495][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.504][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:48.525][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:48.527][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:48.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:48.540][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:48.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:48.544][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:48.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:48.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.558][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:48.583][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:48.585][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:48.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:48.599][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:48.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:48.603][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:48.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:48.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.628][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:48.637][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:48.639][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:48.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:48.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:48.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:48.657][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:48.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:48.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.672][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:48.692][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:48.694][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:48.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:48.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:48.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:48.711][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:48.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:48.717][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.727][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:48.785][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:34:48.793][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 00:34:48.796][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-29 00:34:48.799][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 00:34:48.802][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-08-29 00:34:48.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:48.811][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:48.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:48.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:48.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:48.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:48.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:48.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.843][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:48.861][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:48.863][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:48.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:48.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:48.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:48.880][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:48.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:48.885][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.894][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.903][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.924][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:48.938][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:48.940][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:48.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:48.952][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:48.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:48.956][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:48.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:48.960][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.969][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.979][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:48.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:48.996][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:48.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:49.004][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:49.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:49.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:49.019][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:49.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:49.023][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:49.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:49.028][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.037][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.056][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.066][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:49.075][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:49.078][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:49.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:49.091][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:49.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:49.097][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:49.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:49.102][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.111][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:49.131][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:49.133][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:49.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:49.147][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:49.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:49.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:49.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:49.156][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.167][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:49.186][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:49.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:49.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:49.202][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:49.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:49.206][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:49.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:49.211][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:49.236][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:49.238][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:49.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:49.251][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:49.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:49.256][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:49.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:49.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.269][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.279][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:49.288][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:49.290][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:49.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:49.303][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:49.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:49.307][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:49.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:49.312][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.321][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:49.338][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:49.340][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:49.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:49.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:49.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:49.358][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:49.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:49.363][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.384][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:49.394][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:49.396][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:49.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:49.409][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:49.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:49.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:49.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:49.418][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:49.454][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:49.457][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:49.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:49.469][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:49.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:49.474][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:49.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:49.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:49.505][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:49.507][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:49.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:49.520][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:49.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:49.524][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:49.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:49.528][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:49.559][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:49.561][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:49.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:49.574][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:49.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:49.578][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:49.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:49.581][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.610][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:49.626][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:49.627][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:49.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:49.640][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:49.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:49.643][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:49.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:49.646][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.654][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.663][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:49.671][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:49.673][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:49.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:49.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:49.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:49.690][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:49.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:49.695][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.705][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.714][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:49.724][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:49.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:49.728][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:49.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:49.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:49.744][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:49.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:49.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.759][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:49.778][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:49.780][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:49.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:49.793][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:49.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:49.797][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:49.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:49.802][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:49.830][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:49.832][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:49.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:49.845][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:49.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:49.850][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:49.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:49.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:49.881][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:49.883][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:49.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:49.896][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:49.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:49.901][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:49.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:49.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.916][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.925][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:49.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:49.967][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-29 00:34:49.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-29 00:34:49.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:49.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-29 00:34:49.994][biodb::testThat]
biodb.INFO [2025-08-29 00:34:49.997][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-08-29 00:34:49.999][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 00:34:50.001][biodb::testThat]
biodb.TRACE[2025-08-29 00:34:50.008][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-29 00:34:50.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-29 00:34:50.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.018][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:50.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:50.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.028][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:50.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:50.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.037][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:50.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:50.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.047][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:50.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:50.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:50.062][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:50.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:50.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:50.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:50.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:50.082][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:50.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:50.091][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:34:50.098][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 00:34:50.101][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-08-29 00:34:50.104][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 00:34:50.108][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-08-29 00:34:50.113][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:50.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:50.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:50.128][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:50.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:50.133][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:50.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:50.137][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:50.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:50.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.147][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:50.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:50.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.156][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:50.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:50.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:50.167][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:34:50.174][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 00:34:50.177][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-08-29 00:34:50.180][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 00:34:50.184][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-08-29 00:34:50.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:50.191][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:50.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:50.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:50.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:50.209][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:50.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:50.214][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:50.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:50.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.223][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:50.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:50.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.232][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:50.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:50.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:50.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:50.244][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:50.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:50.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:50.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:50.261][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:50.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:50.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:50.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:50.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.275][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:50.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:50.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:50.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:50.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:50.300][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-29 00:34:50.303][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:50.305][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:50.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:50.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:50.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:50.320][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:50.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:50.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.334][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.343][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:50.345][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 00:34:50.348][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 00:34:50.350][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 00:34:50.352][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:50.354][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.357][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.359][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.361][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.363][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.366][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.368][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.370][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.373][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:50.375][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:50.378][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.380][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.386][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.388][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 00:34:50.390][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.409][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.442][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-08-29 00:34:50.445][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:50.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:50.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:50.459][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:50.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:50.464][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:50.466][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[2025-08-29 00:34:50.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.479][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.489][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:50.491][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 00:34:50.492][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 00:34:50.494][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 00:34:50.496][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:50.498][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.501][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.505][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.508][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.510][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.514][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.516][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:50.519][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:50.520][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.523][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.527][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.529][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 00:34:50.530][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.547][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.556][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-29 00:34:50.559][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:50.561][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:50.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:50.573][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:50.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:50.577][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:50.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:50.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.600][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:50.602][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 00:34:50.604][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 00:34:50.606][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 00:34:50.609][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:50.611][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.614][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.616][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.619][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.621][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.624][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.626][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.629][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.631][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:50.633][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:50.635][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.638][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.640][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.642][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.644][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 00:34:50.647][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:50.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.673][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-08-29 00:34:50.675][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-29 00:34:50.677][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-29 00:34:50.697][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:50.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:50.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:50.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:50.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.715][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:50.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:50.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:50.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:50.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:50.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:50.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:50.867][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:50.869][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:50.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:50.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:50.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:50.884][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:50.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:50.891][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:34:50.898][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:50.901][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:50.905][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-08-29 00:34:51.289][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-08-29 00:34:51.674][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:51.678][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-08-29 00:34:51.688][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-08-29 00:34:51.695][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:34:51.702][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:51.705][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:51.711][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-08-29 00:34:52.096][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-08-29 00:34:52.479][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:52.483][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-08-29 00:34:52.492][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-08-29 00:34:52.499][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:52.501][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:52.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:52.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:52.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:52.519][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:52.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:52.524][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:52.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:52.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:52.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:52.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:52.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:52.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:52.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:52.543][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:52.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:52.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:52.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:52.551][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:52.552][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:52.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:52.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:52.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:52.568][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:52.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:52.572][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:52.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:52.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:52.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:52.598][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:52.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:52.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:52.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:52.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:52.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:52.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:52.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:52.617][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:52.619][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:52.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:52.632][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:52.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:52.636][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:52.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:52.641][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:52.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:52.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:52.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:52.650][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:52.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:52.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:52.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:52.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:52.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:52.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:52.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:52.730][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-29 00:34:52.791][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:52.793][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:52.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:52.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:52.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:52.811][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:52.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:52.817][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:52.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:52.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:52.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:52.826][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:52.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:52.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:52.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:52.835][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:52.837][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 00:34:52.839][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 00:34:52.841][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 00:34:52.843][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:52.845][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:52.847][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:52.849][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:52.852][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:52.854][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:52.856][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:52.858][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:52.860][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:52.862][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:52.864][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:52.867][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:52.869][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:52.871][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:52.874][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:52.876][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 00:34:52.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:52.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:52.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:52.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:52.886][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:52.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:52.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:52.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:52.895][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:52.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:52.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:52.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:52.905][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-08-29 00:34:52.907][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:52.909][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:52.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:52.940][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:52.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:52.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:52.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:52.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:52.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:52.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:52.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:52.991][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:52.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:52.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:52.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.056][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:53.059][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 00:34:53.061][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 00:34:53.063][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 00:34:53.066][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:53.069][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.071][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.076][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.079][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.082][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.086][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.088][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:53.116][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:53.118][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.120][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.122][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.125][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.127][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 00:34:53.130][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.140][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.160][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-29 00:34:53.162][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:53.165][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:53.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:53.178][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:53.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:53.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:53.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:53.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.207][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:53.210][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 00:34:53.212][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 00:34:53.214][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 00:34:53.217][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:53.219][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.222][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.225][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.227][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.230][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.233][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.235][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.238][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.240][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:53.243][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:53.245][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.248][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.251][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.253][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.256][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 00:34:53.258][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.279][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.289][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-08-29 00:34:53.292][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-29 00:34:53.294][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-29 00:34:53.315][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-29 00:34:53.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-29 00:34:53.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-29 00:34:53.331][biodb::testThat]
biodb.INFO [2025-08-29 00:34:53.333][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-08-29 00:34:53.334][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 00:34:53.336][biodb::testThat]
biodb.TRACE[2025-08-29 00:34:53.342][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-29 00:34:53.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-29 00:34:53.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.353][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:53.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:53.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:53.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:53.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.372][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:53.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:53.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.382][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:53.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:53.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:53.398][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:53.400][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:53.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:53.422][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:53.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:53.426][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:53.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:53.434][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:34:53.442][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 00:34:53.445][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-08-29 00:34:53.448][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 00:34:53.451][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-08-29 00:34:53.456][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:53.458][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:53.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:53.472][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:53.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:53.477][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:53.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:53.483][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:53.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:53.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.494][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:53.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:53.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.506][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:53.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:53.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:53.518][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:34:53.527][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 00:34:53.530][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-08-29 00:34:53.534][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 00:34:53.537][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-08-29 00:34:53.544][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:53.546][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:53.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:53.628][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:53.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:53.632][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:53.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:53.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:53.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:53.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.646][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:53.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:53.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:53.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:53.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:53.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:53.667][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:53.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:53.681][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:53.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:53.685][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:53.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:53.689][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:53.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:53.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.698][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:53.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:53.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.708][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:53.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:53.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:53.718][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-29 00:34:53.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:53.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:53.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:53.736][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:53.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:53.740][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:53.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:53.745][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.754][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.765][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:53.767][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 00:34:53.770][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 00:34:53.772][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 00:34:53.774][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:53.776][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.778][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.782][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.785][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.787][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.789][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.791][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.794][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:53.796][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:53.798][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.800][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.804][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.807][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 00:34:53.809][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.818][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.827][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.837][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-08-29 00:34:53.839][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:53.841][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:53.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:53.853][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:53.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:53.857][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:53.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:53.862][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.879][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:53.881][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 00:34:53.883][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 00:34:53.885][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 00:34:53.887][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:53.890][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.892][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.897][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.900][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.903][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.905][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.908][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.911][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:53.914][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:53.916][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.919][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.921][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.923][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.925][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 00:34:53.928][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.937][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.946][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.956][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-29 00:34:53.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:53.961][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:53.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:53.973][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:53.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:53.976][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:53.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:53.980][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.989][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:53.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:53.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:53.999][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:54.001][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 00:34:54.003][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 00:34:54.006][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 00:34:54.008][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:54.011][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.013][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.015][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.017][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.019][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.021][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.026][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.028][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:54.030][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:54.032][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.033][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.035][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.037][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.039][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 00:34:54.041][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.068][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-08-29 00:34:54.071][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-29 00:34:54.073][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-29 00:34:54.092][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:54.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:54.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.101][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:54.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:54.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.110][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:54.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:54.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.118][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:54.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:54.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:54.132][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:54.134][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:54.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:54.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:54.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:54.151][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:54.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:54.158][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:34:54.166][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 00:34:54.170][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-08-29 00:34:54.173][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 00:34:54.175][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-08-29 00:34:54.182][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:34:54.190][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 00:34:54.192][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-08-29 00:34:54.195][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 00:34:54.225][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-08-29 00:34:54.230][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:54.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:54.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:54.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:54.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:54.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:54.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:54.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:54.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:54.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.291][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:54.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:54.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:54.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:54.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:54.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:54.312][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:54.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:54.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:54.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:54.329][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:54.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:54.334][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:54.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:54.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.343][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:54.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:54.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:54.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:54.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:54.370][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:54.372][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:54.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:54.413][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:54.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:54.417][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:54.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:54.422][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:54.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:54.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:54.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:54.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.440][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:54.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:54.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:54.449][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-29 00:34:54.452][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:54.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:54.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:54.465][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:54.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:54.469][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:54.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:54.474][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.483][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.492][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:54.494][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 00:34:54.496][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 00:34:54.499][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 00:34:54.501][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:54.503][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.505][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.508][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.510][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.513][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.515][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.517][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.519][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.522][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:54.524][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:54.526][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.528][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.531][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.533][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.535][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 00:34:54.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.546][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.594][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-08-29 00:34:54.597][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:54.599][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:54.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:54.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:54.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:54.621][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:54.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:54.625][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.643][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:54.645][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 00:34:54.647][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 00:34:54.650][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 00:34:54.652][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:54.654][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.657][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.659][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.661][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.663][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.665][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.668][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.670][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.672][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:54.674][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:54.677][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.679][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.683][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.685][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 00:34:54.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.696][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.705][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.714][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-29 00:34:54.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:54.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:54.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:54.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:54.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:54.767][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:54.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:54.772][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.781][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.790][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:54.793][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 00:34:54.795][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 00:34:54.797][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 00:34:54.799][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:54.801][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.804][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.806][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.808][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.810][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.812][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.814][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.816][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.818][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:54.819][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:54.821][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.823][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.825][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.827][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.830][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 00:34:54.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:54.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.861][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-08-29 00:34:54.863][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-29 00:34:54.865][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-29 00:34:54.882][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-29 00:34:54.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-29 00:34:54.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-29 00:34:54.899][biodb::testThat]
biodb.INFO [2025-08-29 00:34:54.901][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-08-29 00:34:54.904][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 00:34:54.906][biodb::testThat]
biodb.TRACE[2025-08-29 00:34:54.912][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-29 00:34:54.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-29 00:34:54.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.939][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:54.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:54.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.948][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:54.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:54.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.957][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:54.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:54.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:54.967][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:54.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:54.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:54.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:54.986][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:54.989][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:54.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:55.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:55.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:55.005][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:55.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:55.014][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:34:55.023][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 00:34:55.026][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-08-29 00:34:55.030][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 00:34:55.033][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-08-29 00:34:55.039][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:55.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:55.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:55.053][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:55.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:55.057][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:55.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:55.062][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:55.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:55.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.070][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:55.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:55.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.110][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:55.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:55.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:55.121][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:34:55.128][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 00:34:55.131][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-08-29 00:34:55.133][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 00:34:55.136][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-08-29 00:34:55.141][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:55.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:55.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:55.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:55.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:55.161][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:55.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:55.165][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:55.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:55.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.174][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:55.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:55.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.180][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:55.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:55.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:55.190][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:55.192][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:55.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:55.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:55.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:55.209][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:55.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:55.214][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:55.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:55.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.223][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:55.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:55.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.232][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:55.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:55.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:55.241][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-29 00:34:55.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:55.246][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:55.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:55.283][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:55.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:55.288][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:55.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:55.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.303][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.312][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:55.314][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 00:34:55.316][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 00:34:55.319][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 00:34:55.321][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:55.324][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.335][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.337][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.339][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.341][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.343][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.346][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.348][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.350][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:55.353][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:55.355][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.357][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.359][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.361][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.365][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 00:34:55.367][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.385][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.395][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-08-29 00:34:55.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:55.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:55.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:55.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:55.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:55.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:55.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:55.419][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.457][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.467][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:55.469][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 00:34:55.472][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 00:34:55.474][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 00:34:55.476][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:55.478][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.481][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.483][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.486][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.490][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.492][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.497][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.499][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:55.502][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:55.504][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.507][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.509][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.511][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.512][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 00:34:55.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.542][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-29 00:34:55.544][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:55.546][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:55.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:55.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:55.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:55.563][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:55.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:55.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.585][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:55.586][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 00:34:55.588][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 00:34:55.590][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 00:34:55.592][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:55.594][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.596][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.598][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.600][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.603][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.605][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.609][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.612][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:55.614][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:55.616][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.618][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.647][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.649][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 00:34:55.651][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.672][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:55.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.683][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-08-29 00:34:55.685][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-29 00:34:55.687][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-29 00:34:55.734][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:55.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:55.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.744][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:55.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:55.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:55.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:55.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.759][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:55.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:55.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:55.776][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:55.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:55.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:55.791][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:55.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:55.795][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:55.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:55.830][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:34:55.838][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 00:34:55.841][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-08-29 00:34:55.844][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 00:34:55.847][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-08-29 00:34:55.853][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:34:55.861][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 00:34:55.864][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-08-29 00:34:55.866][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 00:34:55.869][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-08-29 00:34:55.875][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:55.876][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:55.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:55.887][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:55.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:55.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:55.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:55.894][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:55.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:55.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.902][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:55.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:55.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:55.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:55.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:55.923][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:55.926][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:55.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:55.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:55.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:55.944][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:55.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:55.948][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:55.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:55.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.957][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:55.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:55.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:55.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:55.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:55.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:55.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:55.977][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:55.979][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:55.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:55.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:55.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:55.996][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:55.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:56.001][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:56.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:56.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:56.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:56.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:56.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:56.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:56.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:56.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:56.054][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-29 00:34:56.058][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:56.060][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:56.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:56.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:56.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:56.078][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:56.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:56.083][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:56.092][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:56.102][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:56.105][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 00:34:56.107][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 00:34:56.110][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 00:34:56.112][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:56.114][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.115][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.120][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:56.122][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.124][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.129][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:56.131][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:56.133][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:56.135][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.137][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.139][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.141][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:56.144][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 00:34:56.146][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:56.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:56.165][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:56.174][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-08-29 00:34:56.176][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:56.178][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:56.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:56.192][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:56.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:56.196][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:56.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:56.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:56.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:56.218][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:56.220][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 00:34:56.222][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 00:34:56.224][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 00:34:56.226][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:56.229][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.231][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.233][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.235][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:56.237][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.263][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.265][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.268][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:56.270][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:56.272][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:56.275][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.278][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.283][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:56.285][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 00:34:56.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:56.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:56.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:56.318][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-29 00:34:56.320][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:56.322][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:56.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:56.335][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:56.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:56.338][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:56.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:56.343][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:56.354][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:56.364][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:56.366][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-29 00:34:56.370][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-29 00:34:56.372][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-29 00:34:56.375][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:56.377][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.380][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.382][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.384][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:56.387][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.390][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.392][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.395][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:56.397][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:56.400][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-29 00:34:56.402][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.405][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.407][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.409][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:56.411][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-29 00:34:56.414][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:56.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:56.432][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:56.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:56.442][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-08-29 00:34:56.445][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-29 00:34:56.447][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-29 00:34:56.494][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-29 00:34:56.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-29 00:34:56.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:56.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-29 00:34:56.509][biodb::testThat]
biodb.INFO [2025-08-29 00:34:56.512][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2025-08-29 00:34:56.515][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 00:34:56.519][biodb::testThat]
biodb.DEBUG[2025-08-29 00:34:56.523][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-08-29 00:34:56.526][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 00:34:56.529][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-08-29 00:34:56.532][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 00:34:56.535][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 00:34:56.537][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:34:56.540][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:34:56.542][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 00:34:56.543][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 00:34:56.549][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:56.551][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:56.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:56.565][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:56.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:56.569][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:56.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:56.574][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-08-29 00:34:56.580][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:56.582][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:56.585][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-08-29 00:34:56.989][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-08-29 00:34:57.374][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:57.378][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-08-29 00:34:57.392][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-08-29 00:34:57.399][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-08-29 00:34:57.403][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 00:34:57.405][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:34:57.408][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:34:57.411][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:57.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:57.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:57.425][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:57.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:57.430][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:57.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:34:57.437][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:57.439][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:57.441][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:57.444][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:57.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:57.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:57.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:57.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:57.455][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:34:57.458][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:34:57.460][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:57.462][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:57.464][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:34:57.467][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:34:57.469][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:57.471][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:57.474][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:34:57.476][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:34:57.478][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:57.480][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:57.483][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:34:57.485][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:34:57.488][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:57.490][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:57.493][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:57.495][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:34:57.498][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:57.500][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:57.503][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:34:57.505][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:34:57.507][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:57.510][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:57.512][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:57.515][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:34:57.517][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:57.519][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:57.522][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:34:57.524][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:34:57.527][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:57.529][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:57.532][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:34:57.534][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:34:57.537][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:57.539][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:57.541][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:34:57.544][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:34:57.546][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:57.548][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:57.550][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:57.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:57.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:57.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:57.556][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:57.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:57.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:57.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:57.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:57.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:57.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:57.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:57.573][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:34:57.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:34:57.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:57.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:57.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:57.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:57.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:57.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:57.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:57.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:57.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:57.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:57.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:57.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:57.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:57.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:57.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:57.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:57.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:57.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:57.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:57.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:57.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:57.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:34:57.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:34:57.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:34:57.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:34:57.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:34:57.623][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-08-29 00:34:57.625][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-08-29 00:34:57.641][biodb::testThat]
biodb.INFO [2025-08-29 00:34:57.643][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-08-29 00:34:57.646][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 00:34:57.648][biodb::testThat]
biodb.DEBUG[2025-08-29 00:34:57.667][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-08-29 00:34:57.670][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-08-29 00:34:57.672][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-08-29 00:34:57.675][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-08-29 00:34:57.678][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-08-29 00:34:57.681][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 00:34:57.683][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:34:57.686][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:34:57.688][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 00:34:57.690][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 00:34:57.700][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:57.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:57.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:57.713][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:57.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:57.717][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:57.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:57.721][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-08-29 00:34:57.726][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:57.728][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:57.731][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-08-29 00:34:58.114][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-08-29 00:34:58.499][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:58.503][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-08-29 00:34:58.525][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-08-29 00:34:58.554][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:58.556][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:58.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:58.569][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:58.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:58.572][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:58.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:58.576][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2025-08-29 00:34:58.580][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:58.583][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:58.586][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2025-08-29 00:34:58.978][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2025-08-29 00:34:59.362][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:34:59.366][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2025-08-29 00:34:59.373][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2025-08-29 00:34:59.378][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:34:59.380][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:34:59.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:34:59.392][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:34:59.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:34:59.396][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:34:59.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:34:59.401][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-08-29 00:34:59.408][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:34:59.410][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:34:59.431][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-08-29 00:34:59.828][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-08-29 00:35:00.213][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:35:00.218][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-08-29 00:35:00.224][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-08-29 00:35:00.230][private$doSaveContentToFile] Saving to cache [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-08-29 00:35:00.235][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 00:35:00.237][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-08-29 00:35:00.239][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-08-29 00:35:00.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:35:00.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:00.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:00.255][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:00.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:00.259][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:00.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:35:00.265][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:00.267][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:00.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.271][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:00.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:00.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.282][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:35:00.284][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:35:00.285][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.287][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.290][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:35:00.292][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:35:00.294][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.296][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.299][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:35:00.301][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:35:00.302][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.303][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.305][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:35:00.307][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:35:00.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.309][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.311][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:35:00.314][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:35:00.315][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.317][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.318][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:35:00.320][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:35:00.321][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.322][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.324][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:35:00.325][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:35:00.327][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.329][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.332][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:35:00.333][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:35:00.335][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.337][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.340][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:35:00.343][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:35:00.345][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.347][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.350][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:35:00.353][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:35:00.355][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.357][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.361][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:35:00.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:35:00.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:35:00.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:35:00.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:00.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:00.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:35:00.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:35:00.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:00.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:00.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:00.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:00.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:00.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:00.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:35:00.410][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:35:00.411][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:00.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:00.420][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:00.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:00.423][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:00.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:35:00.430][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:00.434][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:00.436][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.437][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:00.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:00.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.451][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:35:00.453][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:35:00.456][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.458][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.461][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:35:00.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:35:00.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.470][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:35:00.473][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:35:00.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.477][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.480][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:35:00.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:35:00.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.489][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:35:00.492][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:35:00.494][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.495][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.498][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:35:00.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:35:00.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.506][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:35:00.507][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:35:00.508][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.510][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.513][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:35:00.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:35:00.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.522][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:35:00.524][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:35:00.526][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.528][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.531][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:35:00.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:35:00.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.539][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:35:00.540][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:35:00.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.544][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.547][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:35:00.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:35:00.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.556][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:35:00.559][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:35:00.561][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.563][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:35:00.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:35:00.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.575][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:35:00.577][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:35:00.579][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.581][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:35:00.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:35:00.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.592][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:35:00.594][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:35:00.596][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.599][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.601][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:35:00.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:35:00.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.610][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:35:00.612][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:35:00.614][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.617][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.619][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:35:00.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:35:00.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:35:00.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:35:00.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:35:00.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:35:00.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:00.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:00.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.651][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:35:00.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:35:00.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:00.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:00.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:00.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:00.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:00.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:00.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:35:00.686][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:35:00.688][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:00.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:00.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:00.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:00.704][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:00.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:35:00.710][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:00.713][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:00.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.717][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:00.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:00.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.729][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:35:00.732][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:35:00.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.736][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.739][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:35:00.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:35:00.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.749][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:35:00.750][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:35:00.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.753][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.754][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:35:00.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:35:00.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.762][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:35:00.764][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:35:00.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.766][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.768][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:35:00.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:35:00.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.774][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:35:00.775][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:35:00.776][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.777][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.779][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:35:00.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:35:00.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.785][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:35:00.787][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:35:00.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.789][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.792][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:35:00.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:35:00.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.801][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:35:00.804][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:35:00.806][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.808][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.811][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:35:00.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:35:00.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.821][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:35:00.824][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:35:00.826][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.829][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:35:00.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:35:00.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.841][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:35:00.843][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:35:00.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.847][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.850][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:35:00.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:35:00.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.860][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:35:00.862][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:35:00.865][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.867][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.869][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:35:00.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:35:00.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.877][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:35:00.880][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:35:00.882][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.884][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.887][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:35:00.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:35:00.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.895][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:35:00.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:35:00.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.904][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:35:00.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:35:00.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:00.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:00.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.934][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:35:00.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:35:00.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:00.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:00.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:00.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:00.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:00.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:00.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:00.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:00.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:00.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:00.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:00.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:00.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:00.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:00.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:00.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:01.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:01.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:01.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:01.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:01.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:01.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:01.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:01.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:01.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:01.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:01.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:01.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:01.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:01.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:01.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:01.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:01.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:01.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:01.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:01.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:01.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:01.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:35:01.046][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-08-29 00:35:01.048][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-08-29 00:35:01.050][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-08-29 00:35:01.078][biodb::testThat]
biodb.INFO [2025-08-29 00:35:01.080][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2025-08-29 00:35:01.082][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 00:35:01.085][biodb::testThat]
biodb.INFO [2025-08-29 00:35:01.142][biodb::testThat]
biodb.INFO [2025-08-29 00:35:01.144][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2025-08-29 00:35:01.146][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 00:35:01.148][biodb::testThat]
biodb.INFO [2025-08-29 00:35:01.168][biodb::testThat]
biodb.INFO [2025-08-29 00:35:01.170][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2025-08-29 00:35:01.172][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 00:35:01.174][biodb::testThat]
biodb.DEBUG[2025-08-29 00:35:01.179][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:35:01.187][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:35:01.189][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:35:01.193][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2025-08-29 00:35:01.650][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2025-08-29 00:35:02.118][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:35:02.122][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-08-29 00:35:02.131][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-08-29 00:35:02.160][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:35:02.162][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:35:02.165][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:02.167][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:02.169][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:35:02.171][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:35:02.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:02.176][ef$get] fields variable is a list.
biodb.INFO [2025-08-29 00:35:02.179][biodb::testThat]
biodb.INFO [2025-08-29 00:35:02.181][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2025-08-29 00:35:02.183][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 00:35:02.185][biodb::testThat]
biodb.ERROR[2025-08-29 00:35:02.216][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-08-29 00:35:02.249][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-08-29 00:35:02.279][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-08-29 00:35:02.282][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-08-29 00:35:02.285][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-29 00:35:02.287][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-29 00:35:02.289][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:02.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:02.294][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:02.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:02.298][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:02.300][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.INFO [2025-08-29 00:35:02.324][biodb::testContext]
biodb.INFO [2025-08-29 00:35:02.326][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-29 00:35:02.329][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-08-29 00:35:02.331][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-29 00:35:02.334][biodb::testContext]
biodb.INFO [2025-08-29 00:35:02.338][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-08-29 00:35:02.342][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-29 00:35:02.350][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 00:35:02.352][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-29 00:35:02.355][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-29 00:35:02.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:02.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:02.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:02.364][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-29 00:35:02.407][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-29 00:35:02.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:02.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:02.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:02.415][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-29 00:35:02.417][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-29 00:35:02.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:02.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:02.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:02.425][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-29 00:35:02.427][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-29 00:35:02.429][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-29 00:35:02.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:02.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:02.435][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[2025-08-29 00:35:02.437][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-29 00:35:02.439][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-29 00:35:02.442][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-29 00:35:02.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:02.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:02.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:02.451][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-29 00:35:02.453][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-29 00:35:02.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:02.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:02.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:02.480][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-29 00:35:02.483][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-29 00:35:02.485][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-29 00:35:02.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:02.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:02.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:02.494][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-29 00:35:02.497][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-29 00:35:02.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:02.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:02.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:02.506][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-29 00:35:02.510][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-29 00:35:02.512][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-29 00:35:02.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:02.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:02.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:02.523][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-29 00:35:02.525][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-29 00:35:02.528][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-29 00:35:02.531][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-29 00:35:02.533][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-29 00:35:02.536][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-29 00:35:02.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:02.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:02.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:02.545][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-29 00:35:02.547][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-29 00:35:02.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:02.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:02.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:02.557][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-29 00:35:02.561][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-29 00:35:02.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:02.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:02.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:02.569][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-29 00:35:02.572][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-29 00:35:02.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:02.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:02.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:02.580][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-29 00:35:02.582][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-29 00:35:02.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:02.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:02.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:02.591][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-29 00:35:02.593][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-29 00:35:02.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:02.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:02.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:02.604][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-29 00:35:02.607][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-29 00:35:02.629][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-29 00:35:02.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:02.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:02.637][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[2025-08-29 00:35:02.640][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-29 00:35:02.642][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-29 00:35:02.645][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-29 00:35:02.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:02.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:02.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:02.654][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-29 00:35:02.741][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:02.743][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-29 00:35:02.746][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:02.749][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 00:35:02.751][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:02.754][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 00:35:02.756][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:02.759][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 00:35:02.761][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-29 00:35:02.764][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 00:35:02.766][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:02.769][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-29 00:35:02.774][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 00:35:02.776][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:02.779][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:02.781][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 00:35:02.781][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 00:35:02.781][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 00:35:02.781][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-29 00:35:02.781][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-29 00:35:02.784][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 00:35:02.787][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:02.789][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:02.791][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 00:35:02.793][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:02.795][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:02.798][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 00:35:02.800][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:02.802][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 00:35:02.804][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 00:35:02.846][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:02.848][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:02.851][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-29 00:35:02.855][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:02.893][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-29 00:35:02.896][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:02.898][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 00:35:02.955][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:02.958][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 00:35:02.960][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:02.962][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 00:35:02.965][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-29 00:35:02.970][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 00:35:02.973][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:02.975][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-29 00:35:02.977][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 00:35:02.980][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:02.982][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:02.987][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 00:35:02.987][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 00:35:02.987][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 00:35:02.987][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-29 00:35:02.987][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-29 00:35:02.990][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 00:35:02.995][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:02.998][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:03.000][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 00:35:03.003][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:03.008][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:03.011][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 00:35:03.013][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:03.022][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 00:35:03.024][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 00:35:03.027][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:03.029][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:03.032][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-29 00:35:03.036][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:03.039][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-29 00:35:03.041][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:03.044][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 00:35:03.046][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:03.049][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 00:35:03.052][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:03.054][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 00:35:03.057][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-29 00:35:03.059][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 00:35:03.062][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:03.064][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-29 00:35:03.067][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 00:35:03.070][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:03.072][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:03.075][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:03.077][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 00:35:03.080][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:03.082][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:03.084][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 00:35:03.087][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:03.089][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:03.091][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 00:35:03.094][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:03.097][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 00:35:03.099][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 00:35:03.102][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:03.104][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:03.108][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-29 00:35:03.112][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:03.115][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-29 00:35:03.118][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:03.120][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 00:35:03.123][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:03.126][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 00:35:03.128][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:03.131][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 00:35:03.134][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-29 00:35:03.136][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 00:35:03.138][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:03.140][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-29 00:35:03.143][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 00:35:03.146][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:03.148][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:03.151][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:03.154][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 00:35:03.155][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:03.157][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:03.159][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 00:35:03.161][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:03.163][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:03.165][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 00:35:03.168][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:03.171][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 00:35:03.173][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 00:35:03.176][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:03.179][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:03.182][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 00:35:03.184][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:03.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.198][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[2025-08-29 00:35:03.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.209][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[2025-08-29 00:35:03.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:03.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.229][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[2025-08-29 00:35:03.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.240][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.DEBUG[2025-08-29 00:35:03.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:03.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:03.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.269][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".
biodb.DEBUG[2025-08-29 00:35:03.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.279][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[2025-08-29 00:35:03.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.290][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[2025-08-29 00:35:03.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.300][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[2025-08-29 00:35:03.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:03.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:03.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:03.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:03.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:03.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.364][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[2025-08-29 00:35:03.367][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-29 00:35:03.370][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-29 00:35:03.374][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-29 00:35:03.377][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-29 00:35:03.381][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-29 00:35:03.384][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-29 00:35:03.387][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-29 00:35:03.391][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-29 00:35:03.394][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-29 00:35:03.398][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-29 00:35:03.402][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-29 00:35:03.405][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-29 00:35:03.409][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-29 00:35:03.413][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-29 00:35:03.416][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-29 00:35:03.420][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-29 00:35:03.423][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-29 00:35:03.426][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-29 00:35:03.429][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-29 00:35:03.433][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-29 00:35:03.436][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-29 00:35:03.440][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-29 00:35:03.443][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-29 00:35:03.447][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-29 00:35:03.451][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-29 00:35:03.455][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-29 00:35:03.458][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-29 00:35:03.462][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-29 00:35:03.465][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-29 00:35:03.468][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-29 00:35:03.472][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-29 00:35:03.476][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-29 00:35:03.479][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-29 00:35:03.483][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-29 00:35:03.486][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-29 00:35:03.490][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-29 00:35:03.493][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-29 00:35:03.497][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-29 00:35:03.500][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-29 00:35:03.503][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-29 00:35:03.507][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-29 00:35:03.510][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-29 00:35:03.514][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-29 00:35:03.517][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-29 00:35:03.521][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-29 00:35:03.525][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-29 00:35:03.529][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-29 00:35:03.533][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-29 00:35:03.536][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-29 00:35:03.540][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-29 00:35:03.543][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-29 00:35:03.547][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-29 00:35:03.551][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-29 00:35:03.554][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-29 00:35:03.558][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-29 00:35:03.562][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-29 00:35:03.566][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-29 00:35:03.570][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-29 00:35:03.573][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-29 00:35:03.577][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-29 00:35:03.581][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-29 00:35:03.584][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-29 00:35:03.587][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-29 00:35:03.591][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-29 00:35:03.594][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-29 00:35:03.597][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-29 00:35:03.601][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-29 00:35:03.604][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-29 00:35:03.607][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-29 00:35:03.611][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-29 00:35:03.614][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-29 00:35:03.618][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-29 00:35:03.622][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-29 00:35:03.625][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-29 00:35:03.629][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-29 00:35:03.632][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-29 00:35:03.636][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-29 00:35:03.648][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-29 00:35:03.652][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-29 00:35:03.656][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-29 00:35:03.659][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-29 00:35:03.662][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-29 00:35:03.666][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-29 00:35:03.669][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-29 00:35:03.673][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-08-29 00:35:03.676][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 00:35:03.678][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.682][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:03.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:03.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:03.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:03.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:03.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:03.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:03.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:03.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:03.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:03.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:03.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:03.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:03.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:03.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:03.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:03.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:03.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:03.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:03.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:03.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:03.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:03.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:03.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:03.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.803][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[2025-08-29 00:35:03.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:03.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:03.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:03.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:03.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:03.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:03.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:03.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:03.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:03.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:03.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:03.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:03.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:03.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:03.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:03.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:03.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:03.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:03.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:03.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:03.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:03.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:03.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:03.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:03.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:03.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:03.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:03.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:03.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:03.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:03.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:03.950][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-29 00:35:03.953][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-29 00:35:03.957][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:03.959][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-29 00:35:03.962][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:03.964][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 00:35:03.966][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:03.969][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 00:35:03.971][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:03.974][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-29 00:35:03.976][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-29 00:35:03.979][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 00:35:03.982][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:03.984][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-29 00:35:03.987][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 00:35:03.990][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-29 00:35:03.990][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-29 00:35:03.990][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-29 00:35:03.990][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-29 00:35:03.990][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-29 00:35:03.990][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-29 00:35:03.990][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-29 00:35:03.990][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-29 00:35:03.990][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-29 00:35:03.990][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-29 00:35:03.990][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-29 00:35:03.993][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:03.995][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 00:35:03.995][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 00:35:03.995][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 00:35:03.998][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-29 00:35:04.001][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:04.003][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:04.005][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 00:35:04.007][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:04.010][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:04.012][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 00:35:04.015][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:35:04.015][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-29 00:35:04.017][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 00:35:04.019][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 00:35:04.020][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:04.023][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-29 00:35:04.023][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-29 00:35:04.026][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-29 00:35:04.030][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-29 00:35:04.034][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-29 00:35:04.037][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-29 00:35:04.041][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-29 00:35:04.045][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-29 00:35:04.052][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-29 00:35:04.055][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-08-29 00:35:04.057][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-08-29 00:35:04.061][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-08-29 00:35:04.063][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-29 00:35:04.066][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-29 00:35:04.069][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-08-29 00:35:04.071][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-29 00:35:04.075][biodb::testThat]
biodb.INFO [2025-08-29 00:35:04.077][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2025-08-29 00:35:04.080][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 00:35:04.082][biodb::testThat]
biodb.DEBUG[2025-08-29 00:35:04.091][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.INFO [2025-08-29 00:35:04.100][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2025-08-29 00:35:04.104][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:35:04.106][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:35:04.109][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-08-29 00:35:04.492][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-08-29 00:35:04.961][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:35:04.966][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-08-29 00:35:04.974][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-08-29 00:35:05.029][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:35:05.034][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:35:05.037][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:35:05.040][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-08-29 00:35:05.431][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-08-29 00:35:05.813][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:35:05.818][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-08-29 00:35:05.827][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-08-29 00:35:05.832][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:35:05.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:05.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:05.848][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:05.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:05.852][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:05.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:05.902][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:35:05.910][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:35:05.913][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:35:05.918][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-08-29 00:35:06.318][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-08-29 00:35:06.699][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:35:06.704][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-08-29 00:35:06.738][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-08-29 00:35:06.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:35:06.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:06.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:06.755][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:06.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:06.759][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:06.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:06.802][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:35:06.804][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:06.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:06.816][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:06.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:06.821][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:06.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:06.833][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:35:06.841][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 00:35:06.867][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-08-29 00:35:06.870][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 00:35:06.873][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-08-29 00:35:06.876][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:35:06.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:06.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:06.891][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:06.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:06.895][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:06.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:06.902][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:35:06.909][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 00:35:06.912][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-08-29 00:35:06.916][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 00:35:06.919][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-08-29 00:35:06.923][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:35:06.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:06.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:06.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:06.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:06.943][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:06.945][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.DEBUG[2025-08-29 00:35:06.947][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:35:06.950][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:06.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:06.963][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:06.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:06.967][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:06.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:06.977][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:35:06.984][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 00:35:06.986][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-08-29 00:35:06.989][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 00:35:06.992][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-08-29 00:35:06.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:35:06.997][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:06.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:07.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:07.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:07.014][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:07.015][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[2025-08-29 00:35:07.018][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:35:07.025][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 00:35:07.028][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-08-29 00:35:07.031][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 00:35:07.034][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-08-29 00:35:07.038][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:35:07.040][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:07.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:07.054][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:07.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:07.058][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:07.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:07.065][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:35:07.072][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:35:07.074][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:35:07.079][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-08-29 00:35:07.465][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-08-29 00:35:07.847][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:35:07.851][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-08-29 00:35:07.859][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-08-29 00:35:07.863][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:35:07.866][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:07.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:07.877][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:07.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:07.881][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:07.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-29 00:35:07.897][biodb::testThat]
biodb.INFO [2025-08-29 00:35:07.899][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2025-08-29 00:35:07.902][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 00:35:07.904][biodb::testThat]
biodb.DEBUG[2025-08-29 00:35:07.911][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:35:07.919][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:35:07.922][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:35:07.927][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-08-29 00:35:08.344][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-08-29 00:35:08.729][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:35:08.733][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-08-29 00:35:08.742][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-08-29 00:35:08.747][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:35:08.749][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:08.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:08.763][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:08.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:08.767][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:08.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:08.778][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:35:08.784][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:35:08.786][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:35:08.791][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-08-29 00:35:09.175][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-08-29 00:35:09.553][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:35:09.557][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-08-29 00:35:09.565][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-08-29 00:35:09.569][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:35:09.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:09.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:09.584][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:09.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:09.588][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:09.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-29 00:35:09.602][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-08-29 00:35:09.605][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-08-29 00:35:09.607][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-29 00:35:09.609][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-29 00:35:09.611][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:09.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:09.616][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:09.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:09.620][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:09.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-29 00:35:09.629][biodb::testContext]
biodb.INFO [2025-08-29 00:35:09.631][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-29 00:35:09.634][biodb::testContext] Test context - Test web services
biodb.INFO [2025-08-29 00:35:09.636][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-29 00:35:09.638][biodb::testContext]
biodb.INFO [2025-08-29 00:35:09.643][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-08-29 00:35:09.646][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-29 00:35:09.654][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 00:35:09.656][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-29 00:35:09.659][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-29 00:35:09.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:09.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:09.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:09.667][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-29 00:35:09.670][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-29 00:35:09.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:09.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:09.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:09.678][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-29 00:35:09.680][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-29 00:35:09.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:09.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:09.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:09.689][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-29 00:35:09.691][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-29 00:35:09.694][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-29 00:35:09.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:09.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:09.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:09.701][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-29 00:35:09.704][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-29 00:35:09.706][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-29 00:35:09.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:09.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:09.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:09.715][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-29 00:35:09.717][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-29 00:35:09.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:09.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:09.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:09.726][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-29 00:35:09.728][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-29 00:35:09.730][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-29 00:35:09.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:09.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:09.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:09.738][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-29 00:35:09.740][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-29 00:35:09.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:09.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:09.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:09.749][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-29 00:35:09.750][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-29 00:35:09.752][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-29 00:35:09.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:09.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:09.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:09.761][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-29 00:35:09.764][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-29 00:35:09.766][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-29 00:35:09.768][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-29 00:35:09.770][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-29 00:35:09.773][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-29 00:35:09.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:09.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:09.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:09.781][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-29 00:35:09.783][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-29 00:35:09.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:09.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:09.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:09.791][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-29 00:35:09.794][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-29 00:35:09.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:09.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:09.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:09.802][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-29 00:35:09.804][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-29 00:35:09.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:09.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:09.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:09.813][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-29 00:35:09.816][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-29 00:35:09.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:09.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:09.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:09.824][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-29 00:35:09.827][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-29 00:35:09.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:09.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:09.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:09.836][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-29 00:35:09.839][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-29 00:35:09.856][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-29 00:35:09.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:09.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:09.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:09.865][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-29 00:35:09.867][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-29 00:35:09.869][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-29 00:35:09.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:09.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:09.875][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[2025-08-29 00:35:09.877][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-29 00:35:09.948][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:09.951][self$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[2025-08-29 00:35:09.953][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:09.956][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 00:35:09.959][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:09.961][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 00:35:09.964][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:09.966][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 00:35:09.969][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-29 00:35:09.971][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 00:35:09.973][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:10.001][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-29 00:35:10.003][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 00:35:10.005][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:10.008][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:10.010][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 00:35:10.010][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 00:35:10.010][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 00:35:10.010][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-29 00:35:10.010][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-29 00:35:10.013][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 00:35:10.015][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:10.017][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:10.019][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 00:35:10.021][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:10.023][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:10.026][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 00:35:10.028][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:10.031][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 00:35:10.033][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 00:35:10.035][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:10.037][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:10.040][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-29 00:35:10.044][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:10.047][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-29 00:35:10.049][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:10.051][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 00:35:10.053][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:10.055][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 00:35:10.058][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:10.060][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 00:35:10.063][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-29 00:35:10.065][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 00:35:10.067][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:10.070][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-29 00:35:10.072][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 00:35:10.074][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:10.076][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:10.079][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 00:35:10.079][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 00:35:10.079][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 00:35:10.079][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-29 00:35:10.079][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-29 00:35:10.081][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 00:35:10.084][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:10.086][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:10.088][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 00:35:10.090][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:10.092][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:10.094][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 00:35:10.097][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:10.099][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 00:35:10.101][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 00:35:10.103][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:10.105][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:10.108][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-29 00:35:10.112][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:10.115][self$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[2025-08-29 00:35:10.117][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:10.120][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 00:35:10.122][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:10.124][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 00:35:10.127][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:10.129][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 00:35:10.132][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-29 00:35:10.134][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 00:35:10.137][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:10.139][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-29 00:35:10.141][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 00:35:10.143][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:10.145][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:10.148][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:10.150][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 00:35:10.152][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:10.155][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:10.157][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 00:35:10.159][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:10.161][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:10.163][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 00:35:10.166][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:10.168][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 00:35:10.170][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 00:35:10.172][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:10.174][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:10.177][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-29 00:35:10.180][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:10.182][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-29 00:35:10.185][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:10.187][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 00:35:10.189][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:10.191][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 00:35:10.194][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:10.196][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 00:35:10.198][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-29 00:35:10.200][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 00:35:10.203][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:10.205][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-29 00:35:10.207][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 00:35:10.209][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:10.212][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:10.214][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:10.217][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 00:35:10.219][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:10.221][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:10.223][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 00:35:10.226][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:10.228][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:10.230][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 00:35:10.232][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:10.234][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 00:35:10.237][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 00:35:10.239][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:10.242][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:10.245][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 00:35:10.247][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.249][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.DEBUG[2025-08-29 00:35:10.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.388][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[2025-08-29 00:35:10.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.408][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.DEBUG[2025-08-29 00:35:10.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.417][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[2025-08-29 00:35:10.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.430][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-29 00:35:10.433][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-29 00:35:10.436][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-29 00:35:10.439][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-29 00:35:10.443][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-29 00:35:10.445][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-29 00:35:10.449][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-29 00:35:10.452][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-29 00:35:10.455][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-29 00:35:10.458][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-29 00:35:10.462][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-29 00:35:10.465][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-29 00:35:10.468][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-29 00:35:10.471][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-29 00:35:10.474][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-29 00:35:10.477][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-29 00:35:10.479][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-29 00:35:10.482][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-29 00:35:10.485][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-29 00:35:10.489][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-29 00:35:10.492][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-29 00:35:10.495][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-29 00:35:10.499][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-29 00:35:10.502][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-29 00:35:10.506][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-29 00:35:10.509][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-29 00:35:10.513][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-29 00:35:10.516][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-29 00:35:10.520][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-29 00:35:10.524][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-29 00:35:10.527][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-29 00:35:10.531][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-29 00:35:10.534][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-29 00:35:10.538][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-29 00:35:10.541][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-29 00:35:10.545][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-29 00:35:10.548][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-29 00:35:10.551][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-29 00:35:10.555][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-29 00:35:10.558][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-29 00:35:10.561][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-29 00:35:10.565][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-29 00:35:10.568][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-29 00:35:10.571][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-29 00:35:10.575][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-29 00:35:10.578][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-29 00:35:10.582][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-29 00:35:10.585][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-29 00:35:10.589][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-29 00:35:10.592][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-29 00:35:10.596][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-29 00:35:10.599][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-29 00:35:10.603][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-29 00:35:10.606][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-29 00:35:10.609][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-29 00:35:10.612][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-29 00:35:10.615][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-29 00:35:10.619][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-29 00:35:10.622][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-29 00:35:10.626][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-29 00:35:10.629][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-29 00:35:10.632][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-29 00:35:10.636][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-29 00:35:10.640][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-29 00:35:10.643][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-29 00:35:10.646][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-29 00:35:10.650][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-29 00:35:10.653][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-29 00:35:10.657][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-29 00:35:10.660][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-29 00:35:10.664][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-29 00:35:10.667][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-29 00:35:10.670][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-29 00:35:10.674][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-29 00:35:10.677][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-29 00:35:10.681][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-29 00:35:10.684][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-29 00:35:10.687][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-29 00:35:10.690][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-29 00:35:10.693][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-29 00:35:10.697][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-29 00:35:10.700][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-29 00:35:10.703][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-29 00:35:10.707][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-29 00:35:10.710][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-08-29 00:35:10.713][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 00:35:10.715][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.719][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:10.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:10.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:10.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:10.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:10.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:10.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:10.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:10.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:10.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:10.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:10.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:10.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:10.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:10.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:10.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:10.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:10.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:10.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:10.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:10.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:10.884][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:10.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:10.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:10.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:10.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:10.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:10.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:10.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.936][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[2025-08-29 00:35:10.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:10.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:10.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:10.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:10.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:10.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:10.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:10.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:10.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:10.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:10.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:10.983][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[2025-08-29 00:35:10.987][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-29 00:35:10.991][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-29 00:35:10.995][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:10.997][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-29 00:35:11.000][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:11.002][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 00:35:11.005][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:11.008][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 00:35:11.010][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:11.013][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-29 00:35:11.016][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-29 00:35:11.018][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 00:35:11.021][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:11.023][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-29 00:35:11.025][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 00:35:11.028][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-29 00:35:11.028][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-29 00:35:11.028][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-29 00:35:11.028][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-29 00:35:11.028][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-29 00:35:11.028][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-29 00:35:11.028][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-29 00:35:11.028][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-29 00:35:11.028][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-29 00:35:11.028][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-29 00:35:11.028][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-29 00:35:11.031][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:11.033][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 00:35:11.033][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 00:35:11.033][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 00:35:11.037][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-29 00:35:11.040][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:11.043][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:11.045][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 00:35:11.048][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:11.050][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:11.052][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 00:35:11.055][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:35:11.055][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-29 00:35:11.058][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 00:35:11.060][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 00:35:11.062][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:11.065][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-29 00:35:11.065][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-29 00:35:11.068][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-29 00:35:11.072][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-29 00:35:11.076][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-29 00:35:11.080][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-29 00:35:11.084][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-29 00:35:11.087][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-29 00:35:11.095][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-29 00:35:11.097][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-08-29 00:35:11.100][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-08-29 00:35:11.103][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-08-29 00:35:11.106][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-29 00:35:11.108][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-29 00:35:11.111][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-08-29 00:35:11.114][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-29 00:35:11.117][biodb::testThat]
biodb.INFO [2025-08-29 00:35:11.119][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-08-29 00:35:11.121][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 00:35:11.124][biodb::testThat]
biodb.DEBUG[2025-08-29 00:35:11.131][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-08-29 00:35:11.139][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 00:35:11.142][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-08-29 00:35:11.145][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 00:35:11.148][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-08-29 00:35:11.155][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:35:11.163][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:35:11.165][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:35:11.169][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-08-29 00:35:11.553][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-08-29 00:35:11.935][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:35:11.939][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-08-29 00:35:11.949][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-08-29 00:35:11.967][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-08-29 00:35:11.969][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-08-29 00:35:11.972][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-29 00:35:11.974][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-29 00:35:11.976][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:11.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:11.980][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:11.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:11.985][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:11.987][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.INFO [2025-08-29 00:35:11.994][biodb::testContext]
biodb.INFO [2025-08-29 00:35:11.997][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-29 00:35:11.999][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-08-29 00:35:12.001][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-29 00:35:12.003][biodb::testContext]
biodb.INFO [2025-08-29 00:35:12.007][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-08-29 00:35:12.011][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-29 00:35:12.018][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 00:35:12.021][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-29 00:35:12.023][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-29 00:35:12.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.031][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-29 00:35:12.033][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-29 00:35:12.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.042][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-29 00:35:12.044][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-29 00:35:12.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.052][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-29 00:35:12.054][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-29 00:35:12.057][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-29 00:35:12.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.065][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-29 00:35:12.068][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-29 00:35:12.070][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-29 00:35:12.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.080][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-29 00:35:12.082][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-29 00:35:12.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.090][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-29 00:35:12.093][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-29 00:35:12.096][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-29 00:35:12.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.104][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-29 00:35:12.107][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-29 00:35:12.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.115][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-29 00:35:12.117][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-29 00:35:12.120][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-29 00:35:12.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.128][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-29 00:35:12.131][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-29 00:35:12.133][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-29 00:35:12.135][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-29 00:35:12.138][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-29 00:35:12.140][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-29 00:35:12.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.148][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-29 00:35:12.151][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-29 00:35:12.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.159][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-29 00:35:12.162][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-29 00:35:12.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.170][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-29 00:35:12.172][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-29 00:35:12.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.181][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-29 00:35:12.184][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-29 00:35:12.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.193][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-29 00:35:12.194][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-29 00:35:12.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.202][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-29 00:35:12.205][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-29 00:35:12.222][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-29 00:35:12.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.230][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-29 00:35:12.232][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-29 00:35:12.234][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-29 00:35:12.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.242][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-29 00:35:12.246][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:12.249][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-29 00:35:12.251][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:12.254][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 00:35:12.256][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:12.259][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 00:35:12.262][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:12.264][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 00:35:12.267][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-29 00:35:12.269][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 00:35:12.272][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:12.275][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-29 00:35:12.277][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 00:35:12.280][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:12.282][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:12.285][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 00:35:12.285][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 00:35:12.285][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 00:35:12.285][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-29 00:35:12.285][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-29 00:35:12.287][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 00:35:12.290][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:12.292][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:12.294][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 00:35:12.296][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:12.299][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:12.301][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 00:35:12.303][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:12.305][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 00:35:12.308][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 00:35:12.310][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:12.312][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:12.315][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-29 00:35:12.319][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:12.321][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-29 00:35:12.324][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:12.326][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 00:35:12.328][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:12.331][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 00:35:12.333][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:12.335][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 00:35:12.337][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-29 00:35:12.339][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 00:35:12.342][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:12.344][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-29 00:35:12.360][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 00:35:12.362][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:12.365][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:12.367][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 00:35:12.367][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 00:35:12.367][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 00:35:12.367][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-29 00:35:12.367][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-29 00:35:12.369][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 00:35:12.372][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:12.373][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:12.376][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 00:35:12.378][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:12.380][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:12.382][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 00:35:12.384][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:12.386][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 00:35:12.389][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 00:35:12.391][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:12.393][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:12.396][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-29 00:35:12.400][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:12.402][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-29 00:35:12.404][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:12.407][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 00:35:12.409][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:12.411][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 00:35:12.414][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:12.416][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 00:35:12.418][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-29 00:35:12.420][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 00:35:12.422][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:12.425][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-29 00:35:12.427][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 00:35:12.429][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:12.431][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:12.433][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:12.436][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 00:35:12.438][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:12.440][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:12.442][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 00:35:12.445][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:12.447][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:12.450][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 00:35:12.452][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:12.454][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 00:35:12.457][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 00:35:12.459][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:12.462][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:12.465][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-29 00:35:12.469][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:12.471][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-29 00:35:12.474][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:12.477][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 00:35:12.479][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:12.482][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 00:35:12.484][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:12.487][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-29 00:35:12.489][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-29 00:35:12.491][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 00:35:12.494][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:12.496][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-29 00:35:12.498][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 00:35:12.500][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:12.503][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:12.505][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:12.508][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-29 00:35:12.510][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:12.512][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:12.514][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 00:35:12.516][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:12.519][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:12.521][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 00:35:12.523][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:12.525][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 00:35:12.527][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 00:35:12.530][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:12.532][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-29 00:35:12.535][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 00:35:12.537][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.539][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.DEBUG[2025-08-29 00:35:12.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:12.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:12.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.549][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[2025-08-29 00:35:12.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:12.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:12.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:12.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:12.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:12.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:12.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.582][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[2025-08-29 00:35:12.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:12.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:12.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:12.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:12.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:12.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:12.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.615][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[2025-08-29 00:35:12.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:12.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:12.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:12.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:12.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.636][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[2025-08-29 00:35:12.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:12.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:12.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:12.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:12.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:12.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:12.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:12.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:12.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:12.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:12.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:12.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:12.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:12.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:12.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:12.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:12.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:12.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:12.723][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-29 00:35:12.726][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-29 00:35:12.729][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-29 00:35:12.732][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-29 00:35:12.735][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-29 00:35:12.738][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-29 00:35:12.741][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-29 00:35:12.745][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-29 00:35:12.748][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-29 00:35:12.751][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-29 00:35:12.755][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-29 00:35:12.757][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-29 00:35:12.760][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-29 00:35:12.763][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-29 00:35:12.766][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-29 00:35:12.769][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-29 00:35:12.771][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-29 00:35:12.774][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-29 00:35:12.778][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-29 00:35:12.781][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-29 00:35:12.784][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-29 00:35:12.788][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-29 00:35:12.791][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-29 00:35:12.794][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-29 00:35:12.798][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-29 00:35:12.801][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-29 00:35:12.803][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-29 00:35:12.807][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-29 00:35:12.810][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-29 00:35:12.813][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-29 00:35:12.817][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-29 00:35:12.820][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-29 00:35:12.823][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-29 00:35:12.826][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-29 00:35:12.829][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-29 00:35:12.832][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-29 00:35:12.835][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-29 00:35:12.838][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-29 00:35:12.841][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-29 00:35:12.845][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-29 00:35:12.848][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-29 00:35:12.851][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-29 00:35:12.855][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-29 00:35:12.858][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-29 00:35:12.861][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-29 00:35:12.864][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-29 00:35:12.868][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-29 00:35:12.871][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-29 00:35:12.874][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-29 00:35:12.876][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-29 00:35:12.879][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-29 00:35:12.882][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-29 00:35:12.885][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-29 00:35:12.888][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-29 00:35:12.891][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-29 00:35:12.894][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-29 00:35:12.898][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-29 00:35:12.901][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-29 00:35:12.904][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-29 00:35:12.908][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-29 00:35:12.911][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-29 00:35:12.914][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-29 00:35:12.917][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-29 00:35:12.920][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-29 00:35:12.923][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-29 00:35:12.926][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-29 00:35:12.930][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-29 00:35:12.933][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-29 00:35:12.936][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-29 00:35:12.939][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-29 00:35:12.941][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-29 00:35:12.943][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-29 00:35:12.944][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-29 00:35:12.947][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-29 00:35:12.951][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-29 00:35:12.954][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-29 00:35:12.958][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-29 00:35:12.961][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-29 00:35:12.965][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-29 00:35:12.968][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-29 00:35:12.971][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-29 00:35:12.975][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-29 00:35:12.978][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-29 00:35:12.982][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-29 00:35:12.986][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-08-29 00:35:12.988][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-29 00:35:12.991][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:12.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:12.995][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:12.997][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[2025-08-29 00:35:12.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:13.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:13.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:13.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:13.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:13.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:13.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:13.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:13.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:13.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:13.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:13.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:13.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:13.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:13.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:13.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:13.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:13.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:13.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:13.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:13.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:13.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:13.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:13.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:13.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:13.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:13.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:13.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:13.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:13.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:13.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:13.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:13.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:13.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:13.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:13.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:13.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:13.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:13.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:13.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:13.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:13.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:13.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:13.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:13.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:13.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:13.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:13.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:13.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:13.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:13.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:13.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:13.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:13.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:13.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:13.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:13.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:13.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:13.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:13.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:13.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:13.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:13.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:13.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:13.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:13.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:13.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:13.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:13.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:13.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:13.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:13.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:13.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:13.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:13.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:13.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:13.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:13.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:13.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:13.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:13.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:13.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:13.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:13.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:13.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:13.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:13.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:13.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:13.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:13.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:13.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:13.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:13.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:13.206][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:13.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:13.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:13.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:13.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:13.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:13.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:13.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:13.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:13.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:13.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:13.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:13.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:13.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:13.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:13.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:13.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:13.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:13.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:13.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-29 00:35:13.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:13.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:13.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:13.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:13.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:13.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:13.265][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-29 00:35:13.268][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-29 00:35:13.273][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:13.276][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-29 00:35:13.278][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:13.281][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-29 00:35:13.284][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:13.287][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-29 00:35:13.290][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:13.292][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-29 00:35:13.294][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-29 00:35:13.297][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-29 00:35:13.299][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:13.301][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-29 00:35:13.304][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-29 00:35:13.306][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-29 00:35:13.306][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-29 00:35:13.306][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-29 00:35:13.306][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-29 00:35:13.306][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-29 00:35:13.306][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-29 00:35:13.306][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-29 00:35:13.306][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-29 00:35:13.306][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-29 00:35:13.306][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-29 00:35:13.306][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-29 00:35:13.309][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-29 00:35:13.312][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-29 00:35:13.312][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-29 00:35:13.312][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-29 00:35:13.314][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-29 00:35:13.317][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:13.319][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:13.321][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-29 00:35:13.323][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-29 00:35:13.325][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-29 00:35:13.328][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-29 00:35:13.330][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:35:13.330][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-29 00:35:13.333][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-29 00:35:13.335][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-29 00:35:13.338][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-29 00:35:13.340][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-29 00:35:13.340][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-29 00:35:13.343][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-29 00:35:13.347][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-29 00:35:13.351][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-29 00:35:13.353][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-29 00:35:13.357][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-29 00:35:13.361][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-29 00:35:13.369][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-29 00:35:13.372][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-08-29 00:35:13.376][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-08-29 00:35:13.380][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-08-29 00:35:13.385][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-29 00:35:13.388][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-29 00:35:13.392][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-08-29 00:35:13.395][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-29 00:35:13.398][biodb::testThat]
biodb.INFO [2025-08-29 00:35:13.400][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-08-29 00:35:13.403][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-29 00:35:13.405][biodb::testThat]
biodb.DEBUG[2025-08-29 00:35:13.412][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-08-29 00:35:13.420][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 00:35:13.423][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-08-29 00:35:13.426][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 00:35:13.429][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-08-29 00:35:13.437][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-29 00:35:13.444][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-29 00:35:13.447][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-08-29 00:35:13.451][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-29 00:35:13.454][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-08-29 00:35:13.463][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-08-29 00:35:13.465][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-29 00:35:13.469][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-08-29 00:35:13.472][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-29 00:35:13.475][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-29 00:35:13.478][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-29 00:35:13.480][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-29 00:35:13.483][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-29 00:35:13.485][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-29 00:35:13.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:35:13.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:13.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:13.506][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:13.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:13.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:13.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-29 00:35:13.515][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-08-29 00:35:13.522][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-29 00:35:13.525][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-29 00:35:13.528][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-08-29 00:35:14.300][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-08-29 00:35:14.953][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-29 00:35:14.957][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-08-29 00:35:14.968][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-08-29 00:35:14.974][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-08-29 00:35:14.979][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-29 00:35:14.983][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-29 00:35:14.985][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-29 00:35:14.989][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-29 00:35:14.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:14.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:15.005][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:15.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:15.010][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:15.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-29 00:35:15.022][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:15.024][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:15.027][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.029][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:15.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:15.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.042][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:35:15.045][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:35:15.047][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.049][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.052][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-29 00:35:15.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-29 00:35:15.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.061][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:35:15.064][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:35:15.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.068][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.072][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-29 00:35:15.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-29 00:35:15.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.082][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-29 00:35:15.084][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-29 00:35:15.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.088][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.092][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-29 00:35:15.094][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-29 00:35:15.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.099][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.102][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:35:15.104][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:35:15.107][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.109][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.112][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:35:15.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-29 00:35:15.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.122][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:35:15.125][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:35:15.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.129][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.133][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-29 00:35:15.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-29 00:35:15.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.144][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:35:15.146][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:35:15.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.151][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:35:15.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-29 00:35:15.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.164][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:35:15.167][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:35:15.169][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.172][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.175][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-29 00:35:15.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-29 00:35:15.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.185][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:35:15.187][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:35:15.190][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.192][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.195][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-29 00:35:15.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-29 00:35:15.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.206][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:35:15.208][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:35:15.211][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.213][ef$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.216][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-29 00:35:15.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-29 00:35:15.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:35:15.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:35:15.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:35:15.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:35:15.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:15.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:15.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.256][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-29 00:35:15.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-29 00:35:15.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:15.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:15.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:15.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:15.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:15.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:15.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:15.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:15.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:15.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:15.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-29 00:35:15.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-29 00:35:15.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-29 00:35:15.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-29 00:35:15.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-29 00:35:15.329][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-08-29 00:35:15.338][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-08-29 00:35:15.341][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-08-29 00:35:15.343][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-29 00:35:15.345][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-29 00:35:15.347][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-29 00:35:15.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-29 00:35:15.353][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-29 00:35:15.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-29 00:35:15.357][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-29 00:35:15.359][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
> 
> proc.time()
   user  system elapsed 
 39.715   1.926  77.598

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn 4.480 1.23712.829
ChebiEntry0.6180.0180.642