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This page was generated on 2025-03-10 12:10 -0400 (Mon, 10 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4670
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4355
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4446
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4439
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4306
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 202/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.12.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-03-06 13:00 -0500 (Thu, 06 Mar 2025)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: RELEASE_3_20
git_last_commit: e6b963e
git_last_commit_date: 2024-10-29 11:04:35 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for biodbChebi on kjohnson1

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: 1.12.0
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_1.12.0.tar.gz
StartedAt: 2025-03-07 13:17:57 -0500 (Fri, 07 Mar 2025)
EndedAt: 2025-03-07 13:19:25 -0500 (Fri, 07 Mar 2025)
EllapsedTime: 87.4 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.12.0’
* 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 2.68  1.116    5.17
* 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/4.4-arm64/Resources/library’
* installing *source* package ‘biodbChebi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbChebi)

Tests output

biodbChebi.Rcheck/tests/testthat.Rout


R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 [2025-03-07 13:18:51.844][biodb::testContext]
biodb.INFO [2025-03-07 13:18:51.849][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-07 13:18:51.850][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-03-07 13:18:51.851][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-07 13:18:51.852][biodb::testContext]
biodb.INFO [2025-03-07 13:18:51.861][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-07 13:18:51.863][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-07 13:18:51.873][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 13:18:51.874][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-07 13:18:51.875][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-07 13:18:51.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:51.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:51.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:51.879][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-07 13:18:51.915][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-07 13:18:51.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:51.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:51.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:51.919][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-07 13:18:51.920][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-07 13:18:51.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:51.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:51.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:51.923][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-07 13:18:51.924][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-07 13:18:51.925][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-07 13:18:51.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:51.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:51.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:51.928][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-07 13:18:51.929][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-07 13:18:51.930][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-07 13:18:51.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:51.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:51.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:51.933][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-07 13:18:51.934][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-07 13:18:51.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:51.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:51.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:51.937][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-07 13:18:51.938][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-07 13:18:51.939][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-07 13:18:51.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:51.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:51.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:51.942][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-07 13:18:51.943][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-07 13:18:51.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:51.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:51.946][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[2025-03-07 13:18:51.947][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-07 13:18:51.947][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-07 13:18:51.948][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-07 13:18:51.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:51.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:51.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:51.951][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-07 13:18:51.952][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-07 13:18:51.953][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-07 13:18:51.954][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-07 13:18:51.955][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-07 13:18:51.956][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-07 13:18:51.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:51.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:51.958][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[2025-03-07 13:18:51.959][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-07 13:18:51.960][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-07 13:18:51.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:51.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:51.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:51.963][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-07 13:18:51.963][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-07 13:18:51.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:51.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:51.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:51.966][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-07 13:18:51.967][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-07 13:18:51.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:51.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:51.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:51.970][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-07 13:18:51.971][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-07 13:18:51.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:51.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:51.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:51.974][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-07 13:18:51.975][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-07 13:18:51.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:51.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:51.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:51.978][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-07 13:18:51.979][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-07 13:18:51.997][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-07 13:18:51.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:51.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.001][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-07 13:18:52.002][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-07 13:18:52.003][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-07 13:18:52.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.009][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-07 13:18:52.045][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 13:18:52.063][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-07 13:18:52.064][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 13:18:52.065][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 13:18:52.066][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 13:18:52.067][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 13:18:52.068][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 13:18:52.069][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 13:18:52.070][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-07 13:18:52.071][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 13:18:52.072][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 13:18:52.073][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-07 13:18:52.074][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 13:18:52.075][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:18:52.076][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 13:18:52.077][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 13:18:52.077][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 13:18:52.077][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 13:18:52.077][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-07 13:18:52.077][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-07 13:18:52.078][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 13:18:52.079][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:18:52.080][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:18:52.080][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 13:18:52.088][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:18:52.089][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:18:52.090][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 13:18:52.091][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:18:52.092][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 13:18:52.093][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 13:18:52.094][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 13:18:52.094][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:18:52.095][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-07 13:18:52.097][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 13:18:52.098][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-07 13:18:52.099][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 13:18:52.100][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 13:18:52.101][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 13:18:52.102][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 13:18:52.103][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 13:18:52.104][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 13:18:52.105][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-07 13:18:52.106][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 13:18:52.107][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 13:18:52.108][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-07 13:18:52.109][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 13:18:52.110][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:18:52.111][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 13:18:52.112][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 13:18:52.112][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 13:18:52.112][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 13:18:52.112][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-07 13:18:52.112][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-07 13:18:52.113][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 13:18:52.114][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:18:52.114][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:18:52.115][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 13:18:52.116][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:18:52.117][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:18:52.118][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 13:18:52.119][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:18:52.120][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 13:18:52.120][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 13:18:52.121][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 13:18:52.123][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:18:52.124][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-07 13:18:52.126][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-07 13:18:52.128][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-07 13:18:52.128][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 13:18:52.129][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 13:18:52.130][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 13:18:52.131][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 13:18:52.132][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 13:18:52.133][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 13:18:52.133][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-07 13:18:52.134][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 13:18:52.135][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-07 13:18:52.136][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-07 13:18:52.137][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 13:18:52.137][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:18:52.138][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 13:18:52.139][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:18:52.140][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 13:18:52.141][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:18:52.142][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:18:52.142][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 13:18:52.143][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:18:52.144][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:18:52.145][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 13:18:52.146][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:18:52.146][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 13:18:52.147][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 13:18:52.148][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 13:18:52.149][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:18:52.150][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-07 13:18:52.151][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-07 13:18:52.152][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-07 13:18:52.154][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 13:18:52.155][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 13:18:52.155][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 13:18:52.156][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 13:18:52.157][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 13:18:52.158][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 13:18:52.159][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-07 13:18:52.160][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 13:18:52.160][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-07 13:18:52.161][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-07 13:18:52.162][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 13:18:52.163][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:18:52.164][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 13:18:52.164][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:18:52.165][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 13:18:52.166][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:18:52.167][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:18:52.168][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 13:18:52.169][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:18:52.169][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:18:52.170][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 13:18:52.171][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:18:52.172][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 13:18:52.173][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 13:18:52.174][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 13:18:52.174][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:18:52.179][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 13:18:52.180][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.185][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.DEBUG[2025-03-07 13:18:52.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.199][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[2025-03-07 13:18:52.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.224][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[2025-03-07 13:18:52.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.228][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[2025-03-07 13:18:52.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.235][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[2025-03-07 13:18:52.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.249][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-07 13:18:52.254][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-07 13:18:52.255][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-07 13:18:52.257][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-07 13:18:52.258][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-07 13:18:52.259][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-07 13:18:52.260][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-07 13:18:52.261][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-07 13:18:52.262][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-07 13:18:52.264][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-07 13:18:52.265][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-07 13:18:52.266][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-07 13:18:52.267][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-07 13:18:52.268][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-07 13:18:52.270][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-07 13:18:52.271][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-07 13:18:52.272][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-07 13:18:52.273][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-07 13:18:52.274][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-07 13:18:52.276][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-07 13:18:52.277][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-07 13:18:52.278][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-07 13:18:52.279][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-07 13:18:52.281][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-07 13:18:52.282][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-07 13:18:52.283][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-07 13:18:52.284][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-07 13:18:52.286][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-07 13:18:52.287][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-07 13:18:52.288][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-07 13:18:52.289][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-07 13:18:52.290][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-07 13:18:52.292][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-07 13:18:52.293][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-07 13:18:52.294][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-07 13:18:52.295][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-07 13:18:52.296][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-07 13:18:52.297][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-07 13:18:52.298][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-07 13:18:52.300][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-07 13:18:52.301][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-07 13:18:52.302][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-07 13:18:52.303][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-07 13:18:52.304][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-07 13:18:52.305][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-07 13:18:52.307][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-07 13:18:52.308][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-07 13:18:52.309][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-07 13:18:52.310][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-07 13:18:52.311][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-07 13:18:52.312][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-07 13:18:52.313][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-07 13:18:52.315][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-07 13:18:52.316][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-07 13:18:52.317][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-07 13:18:52.318][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-07 13:18:52.319][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-07 13:18:52.320][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-07 13:18:52.321][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-07 13:18:52.322][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-07 13:18:52.324][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-07 13:18:52.325][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-07 13:18:52.326][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-07 13:18:52.327][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-07 13:18:52.328][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-07 13:18:52.329][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-07 13:18:52.331][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-07 13:18:52.332][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-07 13:18:52.333][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-07 13:18:52.334][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-07 13:18:52.335][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-07 13:18:52.336][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-07 13:18:52.338][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-07 13:18:52.339][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-07 13:18:52.340][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-07 13:18:52.341][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-07 13:18:52.342][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-07 13:18:52.343][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-07 13:18:52.344][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-07 13:18:52.346][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-07 13:18:52.347][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-07 13:18:52.348][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-07 13:18:52.349][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-07 13:18:52.355][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-07 13:18:52.357][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-07 13:18:52.361][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 13:18:52.362][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.363][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.364][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[2025-03-07 13:18:52.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:52.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:52.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:52.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:52.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:52.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:52.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:52.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:52.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.388][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[2025-03-07 13:18:52.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:52.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:52.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:52.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:52.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:52.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:52.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.412][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[2025-03-07 13:18:52.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:52.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:52.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.418][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[2025-03-07 13:18:52.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:52.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:52.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:52.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:52.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:52.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:52.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:52.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:52.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:52.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:52.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:52.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:52.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.449][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[2025-03-07 13:18:52.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:52.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:52.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:52.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:52.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:18:52.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:52.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:52.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:52.466][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-07 13:18:52.477][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-07 13:18:52.479][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 13:18:52.480][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-07 13:18:52.481][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 13:18:52.482][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 13:18:52.483][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 13:18:52.484][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 13:18:52.485][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-07 13:18:52.485][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-07 13:18:52.486][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-07 13:18:52.487][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 13:18:52.488][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 13:18:52.489][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-07 13:18:52.489][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 13:18:52.491][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-07 13:18:52.491][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-07 13:18:52.491][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-07 13:18:52.491][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-07 13:18:52.491][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-07 13:18:52.491][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-07 13:18:52.491][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-07 13:18:52.491][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-07 13:18:52.491][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-07 13:18:52.491][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-07 13:18:52.491][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-07 13:18:52.492][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-07 13:18:52.493][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 13:18:52.493][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 13:18:52.493][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 13:18:52.494][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-07 13:18:52.495][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:18:52.496][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:18:52.497][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 13:18:52.498][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:18:52.498][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:18:52.499][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 13:18:52.500][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:18:52.500][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-07 13:18:52.501][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 13:18:52.501][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 13:18:52.502][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-07 13:18:52.503][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-07 13:18:52.503][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-07 13:18:52.509][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-07 13:18:52.511][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-07 13:18:52.512][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-07 13:18:52.513][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-07 13:18:52.515][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-07 13:18:52.516][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-07 13:18:52.544][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-07 13:18:52.545][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-07 13:18:52.550][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-07 13:18:52.555][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-07 13:18:52.559][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-07 13:18:52.560][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-07 13:18:52.561][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-07 13:18:52.562][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-07 13:18:52.574][biodb::testThat]
biodb.INFO [2025-03-07 13:18:52.575][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-03-07 13:18:52.576][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 13:18:52.576][biodb::testThat]
biodb.TRACE[2025-03-07 13:18:52.582][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-03-07 13:18:52.595][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:18:52.599][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:18:52.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:52.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:52.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:52.626][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:52.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:52.628][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:52.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:18:52.640][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:52.642][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:52.643][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.644][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:52.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:52.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.661][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:18:52.662][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:18:52.663][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.664][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.690][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:18:52.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:18:52.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.694][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:18:52.695][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:18:52.696][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.696][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.698][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:18:52.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:18:52.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.701][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:52.702][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:52.704][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.705][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.706][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:52.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:52.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.710][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:52.711][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:52.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.712][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.714][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:52.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:52.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.717][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:52.718][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:52.719][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.720][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.721][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:52.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:52.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.725][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:18:52.726][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:52.727][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.727][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.728][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:18:52.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:52.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.732][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:52.733][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:52.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.735][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:52.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:52.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.739][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:52.740][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:52.741][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.742][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.743][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:52.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:52.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.747][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:18:52.802][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:18:52.803][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.804][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.805][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:18:52.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:18:52.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.809][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:18:52.810][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:18:52.811][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.811][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.813][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:18:52.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:18:52.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:52.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:52.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.820][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:52.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:52.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:52.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:52.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.827][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:52.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:52.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:52.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:52.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:52.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:52.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:52.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:52.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:52.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:52.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:52.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:52.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:52.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:52.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:18:52.884][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-03-07 13:18:52.887][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:52.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:52.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.890][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:52.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:52.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.916][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:52.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:52.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.926][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:52.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:52.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.930][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:52.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:52.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.933][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:52.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:52.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.936][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-07 13:18:52.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-07 13:18:52.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.939][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-07 13:18:52.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-07 13:18:52.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.943][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-07 13:18:52.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-07 13:18:52.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.946][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-07 13:18:52.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-07 13:18:52.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:52.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:52.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:52.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:52.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:52.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:52.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:52.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:52.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:53.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:53.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:53.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:53.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:53.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:53.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:53.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:53.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:53.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:53.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:53.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:53.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:53.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:53.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.026][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:53.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:53.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:53.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:53.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:53.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:53.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:53.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:53.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.050][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:53.051][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:53.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.053][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:53.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:53.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:53.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:53.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.077][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:53.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:53.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.081][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:53.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:53.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.084][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:53.085][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:53.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.087][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:53.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:53.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.099][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:53.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:53.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.103][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:53.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:53.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.107][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:53.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:53.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.110][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:53.111][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:53.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.113][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.113][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:53.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:53.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.126][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:18:53.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:18:53.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.131][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:18:53.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:18:53.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.134][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:18:53.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:18:53.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.138][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:18:53.139][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:18:53.140][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.140][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.141][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:18:53.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:18:53.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:53.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:53.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:53.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:53.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.161][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:53.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:53.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.165][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:53.166][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:53.167][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.167][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.168][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:53.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:53.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.180][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:53.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:53.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.184][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:53.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:53.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.188][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:53.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:53.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.191][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:53.192][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:53.193][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.193][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.194][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:53.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:53.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.206][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:18:53.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:18:53.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.217][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:18:53.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:18:53.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.221][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:18:53.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:18:53.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.224][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:18:53.225][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:18:53.226][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.226][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.227][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:18:53.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:18:53.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.239][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-07 13:18:53.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:18:53.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.243][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-07 13:18:53.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:18:53.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.246][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-07 13:18:53.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:18:53.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.249][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-07 13:18:53.251][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:18:53.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.253][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.254][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-07 13:18:53.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:18:53.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.267][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:53.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:53.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.271][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:53.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:53.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.275][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:53.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:53.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.278][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:53.279][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:53.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.281][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.281][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:53.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:53.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.294][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:18:53.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:18:53.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.298][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:18:53.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:18:53.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.301][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:18:53.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:18:53.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.305][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:18:53.306][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:18:53.307][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.308][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.309][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:18:53.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:18:53.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.321][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:53.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:53.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.325][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:53.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:53.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.328][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:53.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:53.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.332][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:53.333][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:53.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.334][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.335][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:53.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:53.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.347][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:53.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:53.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.358][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:53.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:53.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.361][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:53.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:53.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.365][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:53.365][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:53.366][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.367][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.368][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:53.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:53.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.379][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:53.381][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:53.381][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.382][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.387][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:18:53.388][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:18:53.389][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.390][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.395][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:18:53.396][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:18:53.397][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.397][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.402][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:53.403][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:53.404][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.405][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.410][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:53.411][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:53.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.413][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.417][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:53.418][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:53.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.420][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.425][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:53.426][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:53.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.428][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.432][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:53.433][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:53.434][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.435][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.440][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-07 13:18:53.441][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:18:53.442][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.443][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.447][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:53.448][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:53.449][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.450][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.455][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:18:53.456][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:18:53.457][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.457][ef$get] fields variable is a list.
biodb.INFO [2025-03-07 13:18:53.465][biodb::testThat]
biodb.INFO [2025-03-07 13:18:53.466][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-07 13:18:53.467][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 13:18:53.468][biodb::testThat]
biodb.DEBUG[2025-03-07 13:18:53.482][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-03-07 13:18:53.491][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 13:18:53.496][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-03-07 13:18:53.497][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 13:18:53.498][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-03-07 13:18:53.500][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:18:53.532][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:18:53.533][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:18:53.535][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:53.535][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:53.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:53.542][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:53.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:53.544][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:53.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:18:53.547][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:53.548][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:53.549][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.550][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:53.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:53.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.571][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:18:53.573][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:18:53.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.575][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.576][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:18:53.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:18:53.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.580][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:18:53.581][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:18:53.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.583][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.584][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:18:53.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:18:53.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.587][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:53.588][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:53.589][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.590][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.591][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:53.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:53.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.594][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:53.595][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:53.596][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.597][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.598][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:53.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:53.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.601][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:53.602][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:53.603][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.604][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.605][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:53.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:53.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.608][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:18:53.609][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:53.610][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.611][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.612][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:18:53.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:53.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.615][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:53.616][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:53.617][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.618][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.619][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:53.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:53.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.622][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:53.623][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:53.624][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.632][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.633][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:53.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:53.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.637][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:18:53.638][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:18:53.639][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.639][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.641][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:18:53.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:18:53.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.644][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:18:53.645][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:18:53.646][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.647][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.648][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:18:53.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:18:53.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.652][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:53.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:53.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.655][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:53.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:53.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:53.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:53.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.662][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:53.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:53.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:53.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:53.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:53.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:53.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:53.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:53.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:53.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:53.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:53.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:53.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:53.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:53.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:18:53.686][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-03-07 13:18:53.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-07 13:18:53.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-07 13:18:53.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.690][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-07 13:18:53.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-07 13:18:53.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.693][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-07 13:18:53.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-07 13:18:53.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-07 13:18:53.705][biodb::testThat]
biodb.INFO [2025-03-07 13:18:53.706][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-07 13:18:53.707][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 13:18:53.708][biodb::testThat]
biodb.TRACE[2025-03-07 13:18:53.711][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:53.712][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:53.713][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.714][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:18:53.715][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-03-07 13:18:53.742][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:53.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:53.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.746][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:53.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:53.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:53.750][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:53.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:53.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:53.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:18:53.763][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-03-07 13:18:53.768][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-07 13:18:53.789][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 13:18:53.805][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-07 13:18:53.807][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 13:18:53.808][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-07 13:18:53.832][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[2025-03-07 13:18:53.836][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:18:53.837][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:18:53.839][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-07 13:18:54.244][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-07 13:18:54.493][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:18:54.495][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-03-07 13:18:54.511][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-03-07 13:18:54.514][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-03-07 13:18:54.527][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:54.528][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:54.529][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:54.530][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:54.531][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:54.531][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:54.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:54.544][ef$get] fields variable is a list.
biodb.INFO [2025-03-07 13:18:54.549][biodb::testThat]
biodb.INFO [2025-03-07 13:18:54.550][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-03-07 13:18:54.551][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 13:18:54.552][biodb::testThat]
biodb.TRACE[2025-03-07 13:18:54.577][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:54.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:54.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:54.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:54.581][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:54.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:54.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:54.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:54.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:54.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:54.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:54.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:18:54.650][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 13:18:54.654][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 13:18:54.655][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-07 13:18:54.656][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 13:18:54.657][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-03-07 13:18:54.675][biodb::testThat]
biodb.INFO [2025-03-07 13:18:54.676][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-03-07 13:18:54.677][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 13:18:54.677][biodb::testThat]
biodb.TRACE[2025-03-07 13:18:54.699][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:54.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:54.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:54.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:54.703][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:54.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:54.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:54.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:54.706][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:54.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:54.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:54.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:54.710][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:54.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:54.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:54.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:54.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:54.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:54.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:54.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:54.716][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:54.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:54.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:54.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:54.719][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-07 13:18:54.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-07 13:18:54.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:54.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:54.723][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-07 13:18:54.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-07 13:18:54.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:54.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:54.726][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-07 13:18:54.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-07 13:18:54.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:54.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:54.729][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-07 13:18:54.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-07 13:18:54.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:54.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:54.757][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:54.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:54.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:54.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:54.761][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:54.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:54.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:54.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:54.765][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:54.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:54.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:54.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:54.768][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:54.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:54.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:54.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:54.772][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:54.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:54.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:54.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:54.775][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:54.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:54.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:54.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:54.778][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-07 13:18:54.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-07 13:18:54.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:54.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:54.781][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-07 13:18:54.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-07 13:18:54.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:54.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:54.784][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-07 13:18:54.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-07 13:18:54.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:54.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:54.788][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-07 13:18:54.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-07 13:18:54.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:54.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-07 13:18:54.800][biodb::testThat]
biodb.INFO [2025-03-07 13:18:54.801][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-07 13:18:54.802][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 13:18:54.803][biodb::testThat]
biodb.INFO [2025-03-07 13:18:54.812][biodb::testThat]
biodb.INFO [2025-03-07 13:18:54.813][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-07 13:18:54.814][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 13:18:54.815][biodb::testThat]
biodb.INFO [2025-03-07 13:18:54.824][biodb::testThat]
biodb.INFO [2025-03-07 13:18:54.825][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-07 13:18:54.825][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 13:18:54.826][biodb::testThat]
biodb.DEBUG[2025-03-07 13:18:54.830][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-03-07 13:18:55.162][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-03-07 13:18:55.595][biodb::testThat]
biodb.INFO [2025-03-07 13:18:55.606][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-07 13:18:55.607][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 13:18:55.608][biodb::testThat]
biodb.DEBUG[2025-03-07 13:18:55.747][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[2025-03-07 13:18:55.890][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:55.891][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:55.892][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:55.893][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:55.894][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:55.895][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:55.896][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:55.896][ef$get] fields variable is a list.
biodb.INFO [2025-03-07 13:18:55.899][biodb::testThat]
biodb.INFO [2025-03-07 13:18:55.900][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-03-07 13:18:55.900][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 13:18:55.901][biodb::testThat]
biodb.TRACE[2025-03-07 13:18:55.913][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:55.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:55.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:55.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:55.918][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:55.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:55.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:55.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:55.922][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:55.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:55.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:55.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:18:56.019][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 13:18:56.022][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 13:18:56.024][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-07 13:18:56.025][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 13:18:56.026][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-07 13:18:56.096][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 13:18:56.100][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 13:18:56.101][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-07 13:18:56.102][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 13:18:56.103][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-03-07 13:18:56.119][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-07 13:18:56.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-07 13:18:56.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:56.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:56.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.131][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:56.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:56.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.134][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:56.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:56.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.137][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:56.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:56.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.141][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:56.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:56.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:18:56.152][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 13:18:56.169][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:18:56.171][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:18:56.194][private$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[2025-03-07 13:18:56.296][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[2025-03-07 13:18:56.399][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:18:56.401][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-03-07 13:18:56.406][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-03-07 13:18:56.409][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:56.410][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:56.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:56.416][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:56.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:56.418][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:56.418][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[2025-03-07 13:18:56.419][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-03-07 13:18:56.474][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 13:18:56.476][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-03-07 13:18:56.477][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 13:18:56.478][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 13:18:56.479][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:18:56.480][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:18:56.481][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 13:18:56.482][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 13:18:56.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:56.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:56.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:56.493][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:56.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:56.495][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:56.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:56.497][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-03-07 13:18:56.500][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:18:56.501][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:18:56.502][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-03-07 13:18:56.620][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-03-07 13:18:56.809][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:18:56.811][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-03-07 13:18:56.816][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-03-07 13:18:56.819][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-03-07 13:18:56.820][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 13:18:56.822][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:18:56.823][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:18:56.824][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:56.825][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:56.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:56.834][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:56.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:56.836][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:56.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:18:56.840][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:56.841][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:56.842][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.842][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:56.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:56.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.847][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:18:56.848][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:18:56.849][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.850][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.851][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:18:56.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:18:56.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.855][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:18:56.855][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:18:56.856][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.857][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.859][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:18:56.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:18:56.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.862][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:56.863][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:56.864][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.865][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.866][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:56.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:56.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.869][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:56.870][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:56.871][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.872][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.880][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:56.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:56.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.887][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:56.888][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:56.889][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.890][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.891][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:18:56.892][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:56.893][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.894][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.895][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:18:56.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:56.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.898][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:56.899][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:56.900][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.901][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.902][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:56.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:56.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.905][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:56.906][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:56.906][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.907][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.908][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:56.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:56.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.912][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:18:56.913][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:18:56.913][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.914][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.915][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:18:56.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:18:56.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.919][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:18:56.919][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:18:56.920][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.921][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.922][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:18:56.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:18:56.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:56.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:56.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.929][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:56.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:56.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:56.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:56.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.936][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:56.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:56.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:56.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:56.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:56.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:56.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:56.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:56.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:56.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:56.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:56.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:56.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:56.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:56.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:18:56.967][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-03-07 13:18:56.977][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:56.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:56.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:56.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:56.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:56.984][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:56.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:56.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:56.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:18:56.989][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[2025-03-07 13:18:56.992][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:18:56.993][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:18:56.995][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-07 13:18:57.094][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-07 13:18:57.194][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:18:57.196][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-03-07 13:18:57.200][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-03-07 13:18:57.217][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:57.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:57.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:57.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:57.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:57.227][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:57.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:18:57.228][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:57.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:57.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.232][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:57.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:57.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:57.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:57.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:18:57.239][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:57.240][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:57.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:57.246][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:57.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:57.257][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:57.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:57.259][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-03-07 13:18:57.260][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 13:18:57.262][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-03-07 13:18:57.263][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 13:18:57.264][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 13:18:57.265][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:18:57.266][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:18:57.267][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 13:18:57.267][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 13:18:57.282][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:57.283][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:57.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:57.290][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:57.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:57.292][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:57.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:57.294][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-03-07 13:18:57.297][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:18:57.298][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:18:57.299][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-03-07 13:18:57.393][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-03-07 13:18:57.491][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:18:57.493][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-03-07 13:18:57.498][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-03-07 13:18:57.500][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-03-07 13:18:57.502][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 13:18:57.503][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:18:57.504][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:18:57.506][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:57.507][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:57.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:57.513][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:57.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:57.515][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:57.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:18:57.518][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:57.519][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:57.520][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.520][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:57.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:57.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.525][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:18:57.526][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:18:57.527][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.527][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.528][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:18:57.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:18:57.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.532][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:18:57.533][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:18:57.543][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.544][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.545][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:18:57.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:18:57.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.548][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:57.549][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:57.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.551][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.552][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:57.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:57.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.555][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:57.556][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:57.557][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.558][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.559][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:57.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:57.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.562][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:57.563][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:57.563][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.564][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.565][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:18:57.566][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:57.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.568][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.569][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:18:57.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:57.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.572][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:57.573][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:57.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.574][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.575][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:57.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:57.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.579][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:57.579][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:57.580][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.581][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.582][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:57.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:57.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.585][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:18:57.586][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:18:57.587][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.588][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.589][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:18:57.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:18:57.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.592][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:18:57.593][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:18:57.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.594][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.595][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:18:57.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:18:57.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:57.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:57.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:57.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:57.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:57.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:57.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:57.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:57.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:57.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:57.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:57.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:57.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:57.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:57.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:57.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:57.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:57.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:57.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:57.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:57.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:18:57.664][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-03-07 13:18:57.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:57.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:57.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.668][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:57.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:57.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.671][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:57.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:57.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:18:57.695][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 13:18:57.698][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 13:18:57.700][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-07 13:18:57.701][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 13:18:57.702][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-07 13:18:57.705][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:57.706][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:57.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:57.712][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:57.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:57.714][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:57.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:18:57.716][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:57.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:57.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.719][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:57.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:57.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:57.723][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:57.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:57.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:57.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:18:57.727][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:57.728][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:57.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:57.735][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:57.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:57.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:57.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:57.738][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-03-07 13:18:57.747][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 13:18:57.749][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-03-07 13:18:57.750][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 13:18:57.752][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 13:18:57.753][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:18:57.754][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:18:57.755][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 13:18:57.756][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 13:18:57.759][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:57.760][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:57.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:57.767][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:57.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:57.768][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:57.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:57.770][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-03-07 13:18:57.773][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:18:57.774][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:18:57.776][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-03-07 13:18:57.880][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-03-07 13:18:57.985][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:18:57.987][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-03-07 13:18:57.991][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-03-07 13:18:57.993][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-03-07 13:18:57.995][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 13:18:57.996][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:18:57.997][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:18:57.999][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:58.000][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:58.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:58.006][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:58.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:58.008][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:58.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:18:58.011][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.012][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.013][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.014][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.019][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:18:58.020][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:18:58.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.021][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.022][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:18:58.023][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:18:58.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.025][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.026][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:58.027][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:58.028][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.028][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.029][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:58.030][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:58.031][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.032][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.033][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:58.034][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:58.035][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.035][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.036][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:18:58.037][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.038][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.039][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.040][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:58.041][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:58.041][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.042][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.043][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:58.053][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:58.055][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.056][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.057][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:58.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:58.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.061][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:18:58.061][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:18:58.062][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.063][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.064][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:18:58.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:18:58.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.067][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:18:58.068][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:18:58.069][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.070][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.071][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:58.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:58.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.074][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:58.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:58.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.081][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:58.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:58.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:18:58.103][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-03-07 13:18:58.104][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.111][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.114][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.117][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:18:58.122][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:58.123][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:58.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:58.130][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:58.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:58.132][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:58.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:58.141][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-03-07 13:18:58.142][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 13:18:58.144][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-03-07 13:18:58.145][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 13:18:58.146][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 13:18:58.147][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:18:58.148][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:18:58.149][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 13:18:58.150][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 13:18:58.153][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:58.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:58.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:58.161][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:58.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:58.163][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:58.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:58.165][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-03-07 13:18:58.168][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:18:58.169][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:18:58.170][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-03-07 13:18:58.286][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-03-07 13:18:58.382][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:18:58.384][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-03-07 13:18:58.389][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-03-07 13:18:58.392][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-03-07 13:18:58.394][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 13:18:58.395][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:18:58.396][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:18:58.398][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:58.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:58.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:58.406][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:58.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:58.407][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:58.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:18:58.411][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.412][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.413][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.414][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.418][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:18:58.419][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:18:58.420][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.421][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.422][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:18:58.423][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:18:58.424][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.425][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.426][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:58.427][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:58.428][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.428][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.429][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:58.430][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:58.431][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.432][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.433][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:58.434][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:58.434][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.435][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.436][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:18:58.437][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.438][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.439][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.440][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:58.441][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:58.442][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.443][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.454][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:58.456][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:58.457][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.458][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.459][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:58.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:58.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.463][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:18:58.464][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:18:58.465][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.465][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.466][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:18:58.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:18:58.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.470][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:18:58.471][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:18:58.471][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.472][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.474][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:58.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:58.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:58.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:58.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.483][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:58.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:58.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:18:58.506][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-03-07 13:18:58.507][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.510][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.514][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.517][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:18:58.526][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:58.527][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:58.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:58.533][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:58.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:58.543][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:58.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:58.545][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-03-07 13:18:58.546][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 13:18:58.548][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-03-07 13:18:58.549][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 13:18:58.550][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 13:18:58.551][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:18:58.552][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:18:58.553][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 13:18:58.554][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 13:18:58.557][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:58.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:58.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:58.566][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:58.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:58.568][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:58.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:58.570][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-03-07 13:18:58.573][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:18:58.574][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:18:58.575][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-03-07 13:18:58.693][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-03-07 13:18:58.792][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:18:58.794][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-03-07 13:18:58.799][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-03-07 13:18:58.802][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-03-07 13:18:58.804][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 13:18:58.805][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:18:58.806][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:18:58.808][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:58.809][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:58.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:58.816][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:58.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:58.818][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:58.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:18:58.823][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.824][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.825][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.826][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.830][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:18:58.831][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:18:58.832][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.833][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.834][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:18:58.835][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:18:58.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.836][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.838][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:58.838][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:58.840][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.841][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.842][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:58.843][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:58.844][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.845][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.846][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:58.847][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:58.848][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.849][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.850][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:18:58.851][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.851][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.852][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.853][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:58.860][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:58.865][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.866][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.868][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:58.869][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:58.869][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.870][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.872][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:58.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:58.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.875][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:18:58.876][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:18:58.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.878][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.879][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:18:58.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:18:58.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.882][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:18:58.883][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:18:58.884][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.885][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.886][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:58.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:58.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.890][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:58.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:58.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:58.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:58.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:58.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:58.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:18:58.923][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-03-07 13:18:58.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.927][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.931][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:58.937][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:58.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:58.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:18:58.941][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:58.941][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:58.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:58.955][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:58.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:58.957][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:58.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:58.960][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-03-07 13:18:58.961][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 13:18:58.963][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-03-07 13:18:58.965][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 13:18:58.966][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 13:18:58.967][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:18:58.968][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:18:58.969][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 13:18:58.969][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 13:18:58.972][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:58.973][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:58.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:58.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:58.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:58.982][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:58.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:58.985][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-03-07 13:18:58.988][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:18:58.989][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:18:58.990][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-03-07 13:18:59.100][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-03-07 13:18:59.200][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:18:59.203][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-03-07 13:18:59.207][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-03-07 13:18:59.210][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-03-07 13:18:59.212][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 13:18:59.213][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:18:59.214][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:18:59.216][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:59.217][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:59.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:59.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:59.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:59.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:59.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:18:59.228][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:59.229][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:59.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.231][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:59.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:59.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.236][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:18:59.237][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:18:59.237][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.238][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.239][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:18:59.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:18:59.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.243][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:18:59.244][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:18:59.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.245][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.247][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:18:59.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:18:59.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.250][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:59.251][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:59.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.253][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.254][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:59.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:59.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.269][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:59.270][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:59.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.271][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.273][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:59.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:59.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.276][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:59.277][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:59.278][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.279][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.280][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:59.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:59.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.284][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:18:59.285][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:59.286][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.286][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.287][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:18:59.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:59.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.291][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:59.292][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:59.293][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.294][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.295][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:59.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:59.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.298][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:59.299][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:59.300][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.301][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.303][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:59.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:59.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.306][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:18:59.307][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:18:59.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.309][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.310][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:18:59.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:18:59.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.313][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:18:59.314][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:18:59.315][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.316][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.317][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:18:59.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:18:59.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.320][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:59.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:59.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.323][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:59.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:59.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:59.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:59.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.330][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:59.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:59.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:59.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:59.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:59.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:59.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:59.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:59.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:59.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:59.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:59.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:59.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:59.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:59.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:18:59.361][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-03-07 13:18:59.362][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:59.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:59.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:59.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:59.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.369][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:59.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:59.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:18:59.372][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:59.373][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:59.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:59.380][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:59.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:59.382][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:59.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:59.383][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-03-07 13:18:59.384][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 13:18:59.386][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-03-07 13:18:59.387][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 13:18:59.388][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 13:18:59.389][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:18:59.390][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:18:59.391][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 13:18:59.392][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 13:18:59.394][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:59.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:59.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:59.401][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:59.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:59.403][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:59.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:59.405][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-03-07 13:18:59.408][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:18:59.409][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:18:59.410][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-03-07 13:18:59.540][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-03-07 13:18:59.640][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:18:59.642][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-03-07 13:18:59.646][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-03-07 13:18:59.649][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-03-07 13:18:59.651][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 13:18:59.652][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:18:59.653][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:18:59.654][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:59.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:59.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:59.662][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:59.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:59.663][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:59.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:18:59.667][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:59.668][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:59.668][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.676][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:59.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:59.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.684][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:18:59.685][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:18:59.686][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.687][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.688][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:18:59.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:18:59.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.691][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:18:59.692][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:18:59.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.694][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.695][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:18:59.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:18:59.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.699][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:59.700][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:59.700][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.701][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.702][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:18:59.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:18:59.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.706][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:59.706][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:59.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.708][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.709][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:18:59.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:18:59.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.712][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:59.713][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:59.714][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.715][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.716][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:59.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:18:59.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.720][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:18:59.721][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:59.721][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.722][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.723][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:18:59.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:59.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.727][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:59.728][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:59.728][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.729][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.730][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:59.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:18:59.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.734][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:59.735][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:59.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.736][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.737][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:18:59.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:18:59.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.741][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:18:59.742][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:18:59.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.743][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.744][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:18:59.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:18:59.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.748][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:18:59.749][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:18:59.749][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.750][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.751][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:18:59.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:18:59.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:59.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:59.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:59.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:59.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:59.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:59.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.773][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:18:59.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:18:59.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:59.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:59.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:59.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:59.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:59.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:59.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:59.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:59.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:59.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:59.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:18:59.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:18:59.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:18:59.797][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-03-07 13:18:59.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:59.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:59.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.802][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:59.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:59.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:18:59.805][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:59.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:18:59.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:18:59.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:18:59.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:59.810][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:59.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:59.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:59.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:59.818][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:59.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:59.820][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-03-07 13:18:59.821][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 13:18:59.823][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-03-07 13:18:59.824][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 13:18:59.825][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 13:18:59.826][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:18:59.827][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:18:59.828][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 13:18:59.829][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 13:18:59.832][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:18:59.832][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:18:59.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:18:59.839][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:18:59.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:18:59.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:18:59.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:18:59.842][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-03-07 13:18:59.845][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:18:59.846][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:18:59.848][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-03-07 13:18:59.958][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-03-07 13:19:00.063][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:00.066][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-03-07 13:19:00.070][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-03-07 13:19:00.073][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-03-07 13:19:00.075][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 13:19:00.076][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:19:00.078][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:19:00.080][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:00.081][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:00.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:00.087][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:00.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:00.089][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:00.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:00.093][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:00.094][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:00.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.095][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:00.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:00.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.100][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:00.102][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:00.103][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.104][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.105][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:00.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:00.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.108][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:00.109][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:00.110][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.111][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.112][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:00.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:00.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.115][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:00.116][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:00.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.118][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.119][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:00.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:00.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.122][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:00.123][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:00.124][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.125][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.126][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:00.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:00.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.130][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:00.130][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:00.131][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.132][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.133][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:00.134][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:00.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.136][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.137][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:00.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:00.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.140][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:00.141][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:00.142][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.143][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.144][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:00.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:00.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.147][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:00.148][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:00.159][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.161][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.162][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:00.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:00.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.166][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:00.167][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:00.168][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.168][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.169][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:00.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:00.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.173][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:00.174][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:00.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.175][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.176][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:00.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:00.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.180][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:00.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:00.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.183][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:00.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:00.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:00.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:00.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.190][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:00.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:00.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:00.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:00.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:00.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:00.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:00.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:00.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:00.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:00.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:00.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:00.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:00.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:00.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:00.213][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-03-07 13:19:00.214][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:00.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:00.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.218][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:00.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:00.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.221][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:00.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:00.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:00.224][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:00.225][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:00.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:00.231][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:00.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:00.233][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:00.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:00.235][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-03-07 13:19:00.236][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 13:19:00.243][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-03-07 13:19:00.245][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 13:19:00.247][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 13:19:00.248][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:19:00.249][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:19:00.250][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 13:19:00.250][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 13:19:00.253][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:00.254][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:00.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:00.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:00.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:00.263][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:00.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:00.265][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-03-07 13:19:00.268][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:00.269][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:00.271][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-03-07 13:19:00.389][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-03-07 13:19:00.491][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:00.493][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-03-07 13:19:00.497][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-03-07 13:19:00.500][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-03-07 13:19:00.502][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 13:19:00.503][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:19:00.504][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:19:00.506][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:00.507][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:00.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:00.514][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:00.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:00.517][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:00.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:00.521][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:00.523][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:00.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.525][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:00.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:00.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.530][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:00.531][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:00.531][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.532][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.533][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:00.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:00.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.537][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:00.538][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:00.538][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.539][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.540][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:00.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:00.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.544][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:00.545][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:00.546][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.546][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.548][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:00.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:00.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.551][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:00.552][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:00.553][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.553][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.554][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:00.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:00.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.797][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:00.798][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:00.799][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.800][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.801][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:00.802][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:00.803][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.803][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.805][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:00.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:00.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.808][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:00.809][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:00.810][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.810][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:00.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:00.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.817][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:00.818][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:00.819][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.820][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.822][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:00.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:00.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.827][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:00.828][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:00.830][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.830][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.832][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:00.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:00.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.838][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:00.839][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:00.840][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.841][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.843][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:00.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:00.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.848][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:00.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:00.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:00.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:00.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:00.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:00.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.863][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:00.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:00.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:00.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:00.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:00.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:00.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:00.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:00.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:00.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:00.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:00.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:00.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:00.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:00.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:00.897][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-03-07 13:19:00.899][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:00.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:00.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.904][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:00.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:00.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:00.908][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:00.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:00.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:00.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:00.911][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:00.912][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:00.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:00.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:00.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:00.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:00.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:00.923][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-03-07 13:19:00.924][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 13:19:00.925][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-03-07 13:19:00.927][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 13:19:00.928][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 13:19:00.929][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:19:00.930][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:19:00.931][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 13:19:00.932][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 13:19:00.935][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:00.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:00.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:00.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:00.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:00.945][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:00.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:00.947][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-03-07 13:19:00.950][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:00.951][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:00.953][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-03-07 13:19:01.065][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-03-07 13:19:01.167][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:01.170][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-03-07 13:19:01.174][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-03-07 13:19:01.178][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-03-07 13:19:01.180][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 13:19:01.182][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:19:01.184][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:19:01.186][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:01.187][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:01.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:01.196][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:01.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:01.199][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:01.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:01.204][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:01.205][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:01.206][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.207][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:01.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:01.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.213][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:01.214][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:01.215][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.215][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.217][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:01.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:01.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.220][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:01.221][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:01.222][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.223][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.225][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:01.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:01.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.229][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:01.231][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:01.232][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.233][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.234][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:01.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:01.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.239][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:01.240][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:01.241][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.242][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.243][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:01.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:01.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.247][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:01.248][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:01.249][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.250][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.251][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:01.253][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:01.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.255][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.256][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:01.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:01.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.260][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:01.261][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:01.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.263][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:01.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:01.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.268][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:01.269][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:01.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.271][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.272][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:01.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:01.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.277][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:01.278][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:01.279][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.280][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.281][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:01.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:01.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.285][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:01.286][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:01.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.288][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.289][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:01.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:01.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:01.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:01.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:01.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:01.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:01.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:01.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:01.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:01.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:01.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:01.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:01.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:01.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:01.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:01.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:01.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:01.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:01.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:01.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:01.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:01.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:01.330][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-03-07 13:19:01.331][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:01.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:01.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.334][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:01.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:01.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.339][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:01.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:01.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:01.343][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:01.344][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:01.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:01.352][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:01.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:01.354][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:01.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:01.356][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-03-07 13:19:01.357][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 13:19:01.359][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-03-07 13:19:01.361][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 13:19:01.362][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 13:19:01.364][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:19:01.365][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:19:01.366][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 13:19:01.366][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 13:19:01.369][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:01.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:01.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:01.377][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:01.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:01.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:01.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:01.382][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-03-07 13:19:01.385][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:01.386][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:01.387][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-03-07 13:19:01.492][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-03-07 13:19:01.631][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:01.634][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-03-07 13:19:01.638][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-03-07 13:19:01.641][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-03-07 13:19:01.658][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 13:19:01.659][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:19:01.661][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:19:01.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:01.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:01.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:01.670][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:01.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:01.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:01.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:01.677][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:01.678][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:01.679][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.680][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:01.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:01.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.686][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:01.687][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:01.689][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.690][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.691][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:01.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:01.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.695][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:01.696][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:01.697][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.697][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.698][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:01.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:01.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.702][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:01.703][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:01.703][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.704][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.705][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:01.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:01.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.708][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:01.709][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:01.710][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.711][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.712][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:01.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:01.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.716][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:01.716][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:01.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.718][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.719][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:01.720][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:01.721][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.721][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.723][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:01.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:01.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.726][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:01.727][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:01.728][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.728][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.730][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:01.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:01.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.733][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:01.734][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:01.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.736][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.737][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:01.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:01.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.741][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:01.742][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:01.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.743][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.744][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:01.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:01.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.748][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:01.749][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:01.749][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.750][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.751][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:01.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:01.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:01.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:01.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.758][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:01.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:01.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:01.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:01.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.765][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:01.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:01.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:01.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:01.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:01.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:01.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:01.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:01.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:01.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:01.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:01.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:01.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:01.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:01.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:01.789][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-03-07 13:19:01.789][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:01.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:01.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.793][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:01.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:01.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:01.796][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:01.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:01.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:01.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:01.800][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:01.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:01.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:01.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:01.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:01.809][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:01.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:01.811][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-03-07 13:19:01.812][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 13:19:01.814][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-03-07 13:19:01.815][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 13:19:01.817][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 13:19:01.818][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:19:01.819][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:19:01.820][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 13:19:01.821][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 13:19:01.824][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:01.825][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:01.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:01.832][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:01.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:01.834][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:01.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:01.836][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-03-07 13:19:01.839][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:01.840][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:01.841][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-03-07 13:19:01.948][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-03-07 13:19:02.044][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:02.047][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-03-07 13:19:02.050][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-03-07 13:19:02.053][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-03-07 13:19:02.055][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 13:19:02.056][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:19:02.057][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:19:02.059][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:02.060][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:02.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:02.067][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:02.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:02.069][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:02.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:02.072][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.073][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.075][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.080][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:02.081][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:02.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.082][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.083][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:02.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:02.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.087][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:02.088][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:02.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.089][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.090][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:02.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:02.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.094][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:02.095][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:02.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.097][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.098][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:02.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:02.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.102][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:02.103][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:02.104][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.105][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.106][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:02.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:02.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.110][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:02.111][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:02.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.113][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.114][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:02.115][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:02.116][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.117][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.118][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:02.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:02.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.122][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:02.123][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:02.124][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.125][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.127][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:02.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:02.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.131][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:02.132][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:02.133][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.134][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.135][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:02.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:02.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.140][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:02.141][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:02.141][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.142][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.144][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:02.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:02.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.147][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:02.148][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:02.149][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.149][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.151][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:02.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:02.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:02.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:02.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.158][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:02.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:02.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.165][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:02.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:02.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:02.189][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-03-07 13:19:02.190][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:02.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:02.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:02.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:02.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.208][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:02.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:02.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:02.212][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:02.213][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:02.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:02.221][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:02.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:02.223][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:02.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:02.225][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-03-07 13:19:02.226][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 13:19:02.227][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-03-07 13:19:02.229][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 13:19:02.230][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 13:19:02.230][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:19:02.231][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:19:02.232][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 13:19:02.233][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 13:19:02.236][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:02.237][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:02.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:02.243][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:02.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:02.245][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:02.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:02.247][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-03-07 13:19:02.249][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:02.250][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:02.252][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-03-07 13:19:02.351][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-03-07 13:19:02.448][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:02.451][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-03-07 13:19:02.455][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-03-07 13:19:02.459][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-03-07 13:19:02.462][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 13:19:02.463][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:19:02.465][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:19:02.467][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:02.468][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:02.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:02.476][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:02.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:02.478][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:02.478][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.TRACE[2025-03-07 13:19:02.481][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.482][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.483][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.484][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.488][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:02.489][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:02.490][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.491][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.492][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:02.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:02.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.495][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:02.496][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:02.497][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.498][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.499][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:02.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:02.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.501][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:02.501][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:02.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.502][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.502][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:02.503][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:02.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.504][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.505][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:02.506][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:02.506][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.507][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.508][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:02.509][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:02.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.511][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.512][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:02.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:02.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.516][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:02.517][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:02.518][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.519][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.520][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:02.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:02.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.523][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:02.524][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:02.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.526][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.527][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:02.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:02.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.532][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:02.533][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:02.533][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.534][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.535][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:02.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:02.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.537][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:02.537][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:02.537][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.538][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.539][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:02.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:02.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.544][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:02.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:02.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.550][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:02.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:02.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:02.574][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-03-07 13:19:02.575][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:02.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:02.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.579][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:02.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:02.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.582][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:02.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:02.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:02.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:02.586][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:02.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:02.593][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:02.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:02.595][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:02.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:02.597][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-03-07 13:19:02.598][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 13:19:02.599][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-03-07 13:19:02.600][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 13:19:02.601][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 13:19:02.602][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:19:02.603][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:19:02.604][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 13:19:02.605][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 13:19:02.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:02.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:02.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:02.615][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:02.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:02.617][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:02.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:02.619][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-03-07 13:19:02.622][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:02.623][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:02.625][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-03-07 13:19:02.726][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-03-07 13:19:02.828][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:02.830][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-03-07 13:19:02.834][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-03-07 13:19:02.836][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-03-07 13:19:02.838][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 13:19:02.839][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:19:02.840][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:19:02.842][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:02.843][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:02.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:02.849][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:02.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:02.852][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:02.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:02.855][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.856][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.857][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.858][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.862][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:02.863][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:02.864][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.865][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.866][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:02.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:02.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.869][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:02.870][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:02.871][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.871][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.873][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:02.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:02.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.876][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:02.877][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:02.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.878][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.879][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:02.880][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:02.881][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.882][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.883][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:02.884][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:02.884][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.885][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.886][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:02.887][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:02.888][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.889][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.890][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:02.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:02.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.893][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:02.894][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:02.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.895][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.896][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:02.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:02.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.900][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:02.900][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:02.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.902][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.903][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:02.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:02.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.906][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:02.907][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:02.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.909][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.910][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:02.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:02.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.913][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:02.914][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:02.915][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.916][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.917][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:02.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:02.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.920][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:02.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:02.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.926][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:02.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:02.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:02.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:02.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:02.964][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-03-07 13:19:02.965][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:02.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:02.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:02.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:02.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:02.971][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:02.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:02.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:02.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:02.975][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:02.976][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:02.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:02.983][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:02.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:02.985][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:02.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:02.986][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-03-07 13:19:02.987][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 13:19:02.989][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-03-07 13:19:02.990][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 13:19:02.991][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 13:19:02.992][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:19:02.993][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:19:02.994][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 13:19:02.995][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 13:19:02.998][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:02.998][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:02.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:03.005][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:03.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:03.007][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:03.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:03.009][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-03-07 13:19:03.012][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:03.013][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:03.015][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-03-07 13:19:03.120][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-03-07 13:19:03.268][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:03.270][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-03-07 13:19:03.274][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-03-07 13:19:03.277][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-03-07 13:19:03.279][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 13:19:03.280][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:19:03.281][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:19:03.283][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:03.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:03.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:03.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:03.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:03.293][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:03.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:03.297][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:03.298][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:03.299][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.300][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:03.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:03.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.305][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:03.306][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:03.307][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.307][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.309][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:03.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:03.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.312][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:03.313][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:03.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.315][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.316][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:03.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:03.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.319][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:03.320][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:03.321][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.321][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.323][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:03.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:03.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.326][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:03.327][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:03.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.328][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.330][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:03.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:03.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.333][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:03.334][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:03.335][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.335][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.337][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:03.338][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:03.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.339][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.340][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:03.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:03.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.343][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:03.344][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:03.345][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.346][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.347][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:03.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:03.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.350][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:03.351][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:03.352][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.353][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.354][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:03.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:03.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.357][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:03.358][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:03.359][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.360][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.361][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:03.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:03.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.364][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:03.365][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:03.366][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.367][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.368][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:03.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:03.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:03.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:03.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.374][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:03.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:03.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:03.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:03.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:03.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:03.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:03.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:03.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:03.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:03.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:03.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:03.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:03.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:03.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:03.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:03.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:03.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:03.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:03.405][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-03-07 13:19:03.406][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:03.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:03.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.411][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:03.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:03.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.415][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:03.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:03.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:03.418][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:03.419][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:03.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:03.426][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:03.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:03.428][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:03.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:03.430][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-03-07 13:19:03.431][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 13:19:03.433][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-03-07 13:19:03.434][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 13:19:03.435][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 13:19:03.436][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:19:03.437][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:19:03.438][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 13:19:03.439][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 13:19:03.442][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:03.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:03.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:03.450][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:03.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:03.452][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:03.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:03.454][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-03-07 13:19:03.457][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:03.459][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:03.460][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-03-07 13:19:03.569][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-03-07 13:19:03.668][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:03.671][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-03-07 13:19:03.675][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-03-07 13:19:03.678][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-03-07 13:19:03.679][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 13:19:03.680][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:19:03.682][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:19:03.683][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:03.684][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:03.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:03.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:03.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:03.692][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:03.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:03.695][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:03.695][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:03.696][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.696][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:03.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:03.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.699][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:03.700][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:03.701][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.702][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.703][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:03.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:03.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.706][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:03.707][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:03.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.709][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.710][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:03.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:03.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.713][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:03.714][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:03.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.716][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.717][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:03.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:03.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.720][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:03.721][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:03.722][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.722][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.723][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:03.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:03.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.727][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:03.728][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:03.728][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.729][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.730][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:03.731][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:03.732][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.733][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.740][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:03.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:03.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.750][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:03.752][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:03.753][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.754][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.755][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:03.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:03.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.758][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:03.759][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:03.760][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.761][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.763][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:03.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:03.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.766][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:03.767][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:03.768][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.768][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.769][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:03.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:03.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.773][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:03.774][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:03.774][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.775][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.776][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:03.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:03.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.780][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:03.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:03.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:03.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:03.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:03.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:03.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.789][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:03.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:03.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:03.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:03.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:03.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:03.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:03.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:03.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:03.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:03.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:03.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:03.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:03.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:03.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:03.812][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-03-07 13:19:03.813][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:03.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:03.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.816][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:03.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:03.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:03.819][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:03.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:03.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:03.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:03.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:03.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:03.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:03.830][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:03.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:03.832][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:03.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:03.834][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-03-07 13:19:03.835][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 13:19:03.836][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-03-07 13:19:03.838][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 13:19:03.839][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 13:19:03.840][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:19:03.841][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:19:03.842][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 13:19:03.842][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 13:19:03.845][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:03.846][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:03.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:03.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:03.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:03.854][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:03.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:03.856][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-03-07 13:19:03.859][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:03.860][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:03.861][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-03-07 13:19:03.964][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-03-07 13:19:04.070][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:04.073][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-03-07 13:19:04.079][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-03-07 13:19:04.082][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-03-07 13:19:04.085][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 13:19:04.086][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:19:04.087][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:19:04.089][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:04.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:04.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:04.097][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:04.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:04.099][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:04.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:04.103][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:04.104][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:04.105][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.106][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:04.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:04.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.111][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:04.112][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:04.113][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.114][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.115][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:04.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:04.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.120][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:04.121][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:04.122][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.123][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.124][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:04.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:04.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.128][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:04.129][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:04.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.130][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.132][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:04.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:04.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.135][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:04.136][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:04.137][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.138][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.139][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:04.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:04.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.142][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:04.143][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:04.144][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.145][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.146][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:04.147][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:04.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.149][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.150][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:04.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:04.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.154][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:04.155][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:04.157][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.157][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:04.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:04.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.164][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:04.165][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:04.167][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.168][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.170][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:04.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:04.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.176][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:04.177][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:04.178][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.179][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.180][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:04.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:04.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.184][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:04.184][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:04.185][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.186][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.187][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:04.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:04.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.191][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:04.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:04.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.194][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:04.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:04.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:04.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:04.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:04.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:04.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:04.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:04.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:04.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:04.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:04.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:04.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:04.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:04.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:04.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:04.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:04.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:04.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:04.225][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-03-07 13:19:04.226][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:04.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:04.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.229][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:04.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:04.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.232][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:04.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:04.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:04.235][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:04.236][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:04.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:04.243][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:04.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:04.244][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:04.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:04.246][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-03-07 13:19:04.247][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 13:19:04.249][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-03-07 13:19:04.250][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 13:19:04.251][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 13:19:04.252][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:19:04.253][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:19:04.254][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 13:19:04.254][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 13:19:04.257][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:04.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:04.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:04.264][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:04.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:04.266][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:04.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:04.268][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-03-07 13:19:04.271][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:04.272][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:04.273][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-03-07 13:19:04.377][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-03-07 13:19:04.483][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:04.486][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-03-07 13:19:04.489][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-03-07 13:19:04.492][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-03-07 13:19:04.493][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 13:19:04.495][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:19:04.496][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:19:04.497][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:04.498][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:04.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:04.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:04.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:04.519][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:04.520][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.TRACE[2025-03-07 13:19:04.522][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:04.523][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:04.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.525][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:04.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:04.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.529][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:04.530][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:04.531][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.532][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.533][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:04.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:04.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.536][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:04.537][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:04.538][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.538][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.540][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:04.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:04.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.543][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:04.544][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:04.544][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.545][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.546][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:04.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:04.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.550][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:04.550][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:04.551][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.552][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.553][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:04.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:04.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.556][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:04.557][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:04.558][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.559][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.560][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:04.561][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:04.561][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.562][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.563][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:04.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:04.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.566][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:04.567][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:04.568][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.569][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:04.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:04.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.573][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:04.574][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:04.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.576][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.577][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:04.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:04.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.580][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:04.581][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:04.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.582][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.583][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:04.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:04.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.587][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:04.587][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:04.588][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.589][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.590][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:04.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:04.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.593][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:04.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:04.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.597][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:04.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:04.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:04.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:04.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:04.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:04.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:04.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:04.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:04.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:04.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:04.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:04.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:04.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:04.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:04.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:04.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:04.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:04.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:04.627][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-03-07 13:19:04.628][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:04.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:04.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.631][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:04.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:04.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.634][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:04.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:04.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:04.638][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:04.638][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:04.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:04.644][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:04.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:04.646][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:04.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:04.648][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-03-07 13:19:04.649][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 13:19:04.650][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-03-07 13:19:04.652][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 13:19:04.653][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 13:19:04.654][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:19:04.655][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:19:04.656][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 13:19:04.656][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 13:19:04.659][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:04.660][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:04.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:04.667][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:04.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:04.669][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:04.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:04.671][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-03-07 13:19:04.674][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:04.675][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:04.676][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-03-07 13:19:04.771][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-03-07 13:19:04.873][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:04.876][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-03-07 13:19:04.880][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-03-07 13:19:04.883][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-03-07 13:19:04.884][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 13:19:04.886][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:19:04.887][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:19:04.888][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:04.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:04.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:04.896][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:04.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:04.897][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:04.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:04.901][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:04.902][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:04.903][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.903][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:04.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:04.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.908][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:04.909][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:04.910][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.910][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.912][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:04.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:04.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.915][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:04.916][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:04.917][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.917][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.919][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:04.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:04.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.923][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:04.923][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:04.924][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.925][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.926][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:04.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:04.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.929][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:04.930][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:04.931][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.932][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.933][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:04.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:04.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.936][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:04.937][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:04.938][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.938][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.940][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:04.940][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:04.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.942][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.943][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:04.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:04.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.946][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:04.947][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:04.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.949][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:04.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:04.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.953][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:04.954][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:04.954][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.955][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.956][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:04.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:04.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.960][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:04.961][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:04.961][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.962][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.963][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:04.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:04.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.967][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:04.967][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:04.968][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.969][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.970][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:04.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:04.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:04.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:04.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:04.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:04.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:04.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:04.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.983][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:04.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:04.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:04.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:04.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:04.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:04.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:04.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:04.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:04.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:04.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:04.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:04.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:05.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:05.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:05.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:05.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:05.007][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-03-07 13:19:05.008][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.012][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.015][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:05.019][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:05.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:05.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:05.037][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:05.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:05.039][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:05.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:05.040][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-03-07 13:19:05.041][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 13:19:05.043][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-03-07 13:19:05.045][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 13:19:05.046][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 13:19:05.047][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:19:05.047][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:19:05.048][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 13:19:05.049][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 13:19:05.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:05.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:05.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:05.060][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:05.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:05.062][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:05.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:05.064][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-03-07 13:19:05.067][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:05.068][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:05.069][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-03-07 13:19:05.167][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-03-07 13:19:05.270][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:05.272][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-03-07 13:19:05.276][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-03-07 13:19:05.279][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-03-07 13:19:05.280][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 13:19:05.281][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:19:05.282][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:19:05.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:05.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:05.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:05.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:05.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:05.293][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:05.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:05.297][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:05.298][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:05.299][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.300][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:05.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:05.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.304][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:05.305][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:05.306][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.307][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.308][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:05.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:05.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.311][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:05.312][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:05.313][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.313][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.315][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:05.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:05.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.318][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:05.319][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:05.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.321][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.322][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:05.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:05.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.325][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:05.326][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:05.327][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.327][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.328][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:05.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:05.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.332][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:05.333][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:05.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.334][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.336][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:05.337][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.337][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.338][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.339][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:05.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.343][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:05.344][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:05.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.345][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.346][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:05.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:05.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.350][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:05.350][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:05.351][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.352][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.353][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:05.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:05.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.357][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:05.357][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:05.358][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.359][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.360][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:05.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:05.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.363][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:05.364][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:05.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.366][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.367][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:05.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:05.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.370][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:05.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:05.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:05.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:05.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:05.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:05.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.380][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:05.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:05.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:05.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:05.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:05.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:05.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:05.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:05.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:05.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:05.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:05.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:05.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:05.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:05.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:05.404][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-03-07 13:19:05.406][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.412][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:05.415][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:05.416][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:05.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:05.422][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:05.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:05.424][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:05.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:05.426][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-03-07 13:19:05.427][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 13:19:05.428][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-03-07 13:19:05.430][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 13:19:05.431][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 13:19:05.431][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:19:05.432][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:19:05.433][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 13:19:05.434][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 13:19:05.437][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:05.438][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:05.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:05.444][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:05.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:05.446][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:05.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:05.448][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-03-07 13:19:05.450][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:05.451][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:05.453][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-03-07 13:19:05.561][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-03-07 13:19:05.665][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:05.668][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-03-07 13:19:05.674][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-03-07 13:19:05.677][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-03-07 13:19:05.679][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 13:19:05.681][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:19:05.682][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:19:05.683][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:05.684][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:05.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:05.691][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:05.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:05.693][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:05.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:05.696][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:05.697][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:05.698][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.699][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:05.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:05.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.704][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:05.705][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:05.705][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.706][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.707][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:05.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:05.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.711][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:05.712][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:05.712][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.713][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.714][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:05.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:05.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.718][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:05.719][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:05.720][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.720][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.722][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:05.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:05.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.725][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:05.726][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:05.727][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.727][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.729][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:05.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:05.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.732][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:05.733][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:05.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.735][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.736][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:05.737][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.738][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.739][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.741][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:05.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.746][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:05.747][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:05.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.749][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:05.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:05.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.755][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:05.756][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:05.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.759][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.761][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:05.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:05.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.766][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:05.767][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:05.768][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.769][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.771][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:05.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:05.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.776][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:05.777][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:05.778][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.779][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.780][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:05.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:05.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.793][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:05.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:05.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:05.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:05.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:05.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:05.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:05.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:05.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:05.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:05.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:05.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:05.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:05.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:05.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:05.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:05.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:05.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:05.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:05.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:05.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:05.836][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-03-07 13:19:05.837][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.840][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.843][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:05.866][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 13:19:05.870][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 13:19:05.871][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-07 13:19:05.873][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 13:19:05.874][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-07 13:19:05.878][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:05.879][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:05.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:05.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:05.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:05.887][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:05.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:05.889][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.892][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.897][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:05.900][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:05.901][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:05.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:05.908][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:05.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:05.909][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:05.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:05.911][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.918][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.922][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.925][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:05.928][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:05.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:05.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:05.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:05.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:05.937][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:05.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:05.939][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.942][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.946][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.952][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:05.956][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:05.956][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:05.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:05.962][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:05.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:05.964][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:05.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:05.966][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.977][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:05.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:05.985][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:05.985][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:05.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:05.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:05.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:05.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:05.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:05.996][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:05.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:05.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.000][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.003][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:06.007][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:06.007][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:06.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:06.014][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:06.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:06.015][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:06.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:06.017][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.021][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.024][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:06.027][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:06.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:06.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:06.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:06.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:06.036][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:06.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:06.038][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.042][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.045][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:06.049][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:06.050][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:06.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:06.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:06.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:06.058][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:06.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:06.060][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.066][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:06.070][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:06.071][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:06.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:06.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:06.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:06.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:06.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:06.081][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.084][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.087][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:06.091][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:06.091][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:06.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:06.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:06.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:06.099][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:06.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:06.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.105][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:06.112][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:06.113][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:06.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:06.119][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:06.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:06.121][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:06.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:06.123][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.130][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:06.133][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:06.134][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:06.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:06.152][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:06.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:06.154][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:06.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:06.156][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.160][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.163][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:06.166][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:06.167][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:06.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:06.173][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:06.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:06.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:06.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:06.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.181][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.184][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:06.187][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:06.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:06.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:06.194][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:06.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:06.196][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:06.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:06.198][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.201][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.204][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:06.207][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:06.208][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:06.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:06.214][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:06.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:06.216][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:06.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:06.218][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.221][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.225][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:06.228][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:06.229][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:06.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:06.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:06.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:06.237][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:06.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:06.239][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.243][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.246][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:06.250][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:06.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:06.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:06.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:06.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:06.258][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:06.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:06.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.263][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.267][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:06.270][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:06.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:06.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:06.277][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:06.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:06.278][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:06.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:06.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:06.290][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:06.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:06.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:06.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:06.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:06.299][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:06.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:06.300][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.304][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.307][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:06.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:06.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:06.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:06.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:06.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:06.319][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:06.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:06.321][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.325][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.328][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:06.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:06.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:06.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.352][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:06.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:06.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:06.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:06.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.358][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:06.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:06.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:06.362][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:06.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:06.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:06.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:06.391][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 13:19:06.395][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:06.396][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:06.398][private$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[2025-03-07 13:19:06.491][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[2025-03-07 13:19:06.593][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:06.595][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-03-07 13:19:06.600][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-03-07 13:19:06.605][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[2025-03-07 13:19:06.608][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:06.609][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:06.611][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-07 13:19:06.706][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-07 13:19:06.807][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:06.809][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-03-07 13:19:06.812][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-03-07 13:19:06.815][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:06.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:06.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:06.822][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:06.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:06.823][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:06.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:06.824][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-03-07 13:19:06.825][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 13:19:06.826][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-03-07 13:19:06.827][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 13:19:06.827][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 13:19:06.828][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:19:06.828][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:19:06.829][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 13:19:06.829][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 13:19:06.832][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:06.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:06.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:06.840][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:06.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:06.842][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:06.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:06.844][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-03-07 13:19:06.847][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:06.848][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:06.849][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-03-07 13:19:07.007][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-03-07 13:19:07.112][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:07.115][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-03-07 13:19:07.119][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-03-07 13:19:07.121][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-03-07 13:19:07.123][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 13:19:07.124][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:19:07.125][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:19:07.127][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:07.128][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:07.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:07.150][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:07.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:07.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:07.153][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.TRACE[2025-03-07 13:19:07.156][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:07.158][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:07.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.159][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:07.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:07.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.164][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:07.165][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:07.165][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.166][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.167][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:07.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:07.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.171][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:07.172][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:07.172][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.173][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.175][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:07.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:07.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.178][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:07.179][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:07.180][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.180][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.182][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:07.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:07.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.185][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:07.186][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:07.186][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.187][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.188][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:07.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:07.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.192][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:07.193][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:07.193][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.194][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.195][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:07.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:07.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.199][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:07.199][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:07.200][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.201][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.202][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:07.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:07.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.205][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:07.206][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:07.207][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.208][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.209][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:07.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:07.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.212][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:07.213][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:07.214][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.215][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.216][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:07.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:07.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.220][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:07.220][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:07.221][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.222][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.223][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:07.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:07.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.227][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:07.228][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:07.228][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.229][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.230][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:07.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:07.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.234][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:07.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:07.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.237][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:07.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:07.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:07.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:07.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:07.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:07.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:07.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:07.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:07.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:07.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:07.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:07.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:07.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:07.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:07.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:07.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:07.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:07.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:07.266][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-03-07 13:19:07.267][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:07.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:07.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.271][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:07.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:07.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:07.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:07.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:07.277][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:07.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:07.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:07.284][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:07.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:07.286][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:07.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:07.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:07.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:07.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:07.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:07.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.295][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:07.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:07.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:07.299][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:07.299][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:07.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:07.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:07.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:07.309][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:07.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:07.311][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-03-07 13:19:07.312][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 13:19:07.314][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-03-07 13:19:07.315][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 13:19:07.316][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 13:19:07.317][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:19:07.318][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:19:07.319][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 13:19:07.320][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 13:19:07.323][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:07.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:07.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:07.331][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:07.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:07.332][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:07.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:07.334][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-03-07 13:19:07.338][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:07.339][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-07 13:19:07.340][rule$waitAsNeeded] Wait 0.057796 second(s).
biodb.TRACE[2025-03-07 13:19:07.549][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-03-07 13:19:07.649][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-03-07 13:19:07.809][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:07.811][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-03-07 13:19:07.815][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-03-07 13:19:07.818][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-03-07 13:19:07.819][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 13:19:07.821][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:19:07.822][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:19:07.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:07.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:07.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:07.830][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:07.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:07.832][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:07.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:07.835][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:07.837][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:07.838][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.839][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:07.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:07.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.844][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:07.845][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:07.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.846][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.847][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:07.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:07.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.851][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:07.852][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:07.853][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.854][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.855][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:07.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:07.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.858][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:07.859][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:07.860][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.861][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.862][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:07.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:07.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.865][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:07.866][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:07.867][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.868][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.869][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:07.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:07.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.872][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:07.873][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:07.874][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.875][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.876][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:07.877][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:07.878][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.879][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.880][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:07.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:07.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.883][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:07.884][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:07.885][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.886][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:07.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:07.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.890][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:07.891][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:07.892][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.893][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.894][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:07.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:07.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.898][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:07.900][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:07.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.902][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.903][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:07.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:07.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.907][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:07.907][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:07.908][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.909][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.910][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:07.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:07.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:07.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:07.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.917][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:07.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:07.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:07.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:07.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:07.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:07.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:07.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:07.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:07.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:07.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:07.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:07.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:07.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:07.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:07.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:07.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:07.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:07.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:07.957][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-03-07 13:19:07.958][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:07.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:07.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:07.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:07.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:07.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:07.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:07.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:07.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:07.989][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[2025-03-07 13:19:07.993][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 13:19:07.994][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-07 13:19:07.996][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 13:19:07.997][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-07 13:19:08.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.001][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.010][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:08.012][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.019][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.022][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:08.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.037][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.051][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.060][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.061][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.TRACE[2025-03-07 13:19:08.062][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.065][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.079][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.085][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.088][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:08.091][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.105][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.109][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.124][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.127][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[2025-03-07 13:19:08.129][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.134][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.143][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.152][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.154][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:08.156][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.167][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.167][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.174][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.176][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[2025-03-07 13:19:08.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.184][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.188][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.197][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[2025-03-07 13:19:08.198][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.202][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.206][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.209][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.210][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.216][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.218][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:08.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.227][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.230][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.231][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.237][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.239][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:08.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.244][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.251][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.252][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.258][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.260][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.261][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.TRACE[2025-03-07 13:19:08.262][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.265][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.269][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.272][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.273][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.279][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.282][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[2025-03-07 13:19:08.283][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.286][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.290][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.293][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.310][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:08.312][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.315][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.319][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.329][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.331][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.332][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[2025-03-07 13:19:08.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.336][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.340][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.343][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.344][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.352][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:08.354][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.358][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.361][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.364][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.365][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.371][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.373][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:08.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.378][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.385][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.392][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.395][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.395][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[2025-03-07 13:19:08.397][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.400][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.404][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.408][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.408][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.415][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.417][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.418][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.TRACE[2025-03-07 13:19:08.419][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.422][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.426][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.429][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:08.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.451][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.458][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:08.461][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.465][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.468][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.491][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[2025-03-07 13:19:08.495][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 13:19:08.497][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-07 13:19:08.498][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 13:19:08.499][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-07 13:19:08.503][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.504][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.510][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.512][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.513][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.TRACE[2025-03-07 13:19:08.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.520][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.524][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.525][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.530][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.532][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.533][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.TRACE[2025-03-07 13:19:08.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.537][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.544][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.550][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.551][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.559][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.560][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.TRACE[2025-03-07 13:19:08.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.564][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.571][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.577][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.584][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.586][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:08.587][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.591][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.597][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.601][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.604][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.605][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.611][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.612][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:08.614][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.621][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.633][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:08.634][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.638][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.641][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.652][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.653][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.659][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.661][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:08.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.672][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.673][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.679][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.681][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:08.683][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.693][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.693][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.699][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.701][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:08.703][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.709][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.713][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.713][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.719][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.721][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:08.723][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.733][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.733][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.741][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.742][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[2025-03-07 13:19:08.743][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.750][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.753][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.762][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:08.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.781][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.783][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:08.785][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.803][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.804][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.TRACE[2025-03-07 13:19:08.805][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.815][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.822][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.824][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:08.826][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.836][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.837][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.845][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:08.847][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.855][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.866][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.868][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:08.870][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.873][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.876][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.880][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.887][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.889][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:08.891][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.895][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.902][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.902][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.909][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.911][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:08.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.916][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.919][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:08.923][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:08.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:08.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:08.930][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:08.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:08.932][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:08.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:08.934][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:08.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.961][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-07 13:19:08.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-07 13:19:08.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-07 13:19:08.973][biodb::testThat]
biodb.INFO [2025-03-07 13:19:08.974][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-03-07 13:19:08.975][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 13:19:08.976][biodb::testThat]
biodb.TRACE[2025-03-07 13:19:08.979][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-07 13:19:08.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-07 13:19:08.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.983][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:08.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:08.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.986][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:08.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:08.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:08.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:08.997][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:08.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:08.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.000][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:09.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:09.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:09.007][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:09.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:09.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:09.014][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:09.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:09.016][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:09.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:09.019][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[2025-03-07 13:19:09.023][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 13:19:09.024][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-07 13:19:09.025][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 13:19:09.027][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-07 13:19:09.029][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:09.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:09.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:09.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:09.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:09.038][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:09.039][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.TRACE[2025-03-07 13:19:09.040][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:09.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:09.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.043][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:09.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:09.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.047][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:09.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:09.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:09.051][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[2025-03-07 13:19:09.054][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 13:19:09.056][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-07 13:19:09.057][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 13:19:09.058][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-07 13:19:09.061][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:09.062][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:09.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:09.068][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:09.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:09.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:09.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:09.072][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:09.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:09.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.075][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:09.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:09.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:09.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:09.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:09.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:09.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:09.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:09.089][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:09.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:09.091][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:09.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:09.092][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:09.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:09.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.096][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:09.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:09.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.099][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:09.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:09.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:09.103][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-07 13:19:09.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:09.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:09.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:09.112][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:09.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:09.113][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:09.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:09.115][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.119][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.122][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:09.123][private$selectFields]
biodb.TRACE[2025-03-07 13:19:09.123][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 13:19:09.124][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 13:19:09.125][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:09.126][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.127][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.128][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.129][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.130][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.131][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.132][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:09.133][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:09.134][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.134][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.136][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.137][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 13:19:09.138][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.141][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.144][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.156][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-07 13:19:09.158][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:09.159][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:09.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:09.166][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:09.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:09.168][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:09.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:09.170][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.177][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:09.178][private$selectFields]
biodb.TRACE[2025-03-07 13:19:09.179][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 13:19:09.180][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 13:19:09.180][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:09.181][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.182][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.183][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.184][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.184][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.185][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.186][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.187][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.188][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:09.189][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:09.190][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.191][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.191][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.192][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.193][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 13:19:09.194][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.197][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.204][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-07 13:19:09.205][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:09.206][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:09.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:09.213][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:09.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:09.215][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:09.215][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.TRACE[2025-03-07 13:19:09.216][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.220][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.224][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:09.225][private$selectFields]
biodb.TRACE[2025-03-07 13:19:09.225][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 13:19:09.226][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 13:19:09.227][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:09.228][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.229][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.230][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.231][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.232][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.233][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.234][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.234][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:09.235][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:09.236][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.237][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.238][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.238][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.239][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 13:19:09.240][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.246][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.250][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-07 13:19:09.251][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-07 13:19:09.252][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-07 13:19:09.262][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:09.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:09.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:09.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:09.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.269][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:09.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:09.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.272][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:09.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:09.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:09.337][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:09.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:09.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:09.345][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:09.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:09.346][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:09.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:09.350][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[2025-03-07 13:19:09.354][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:09.355][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:09.357][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-07 13:19:09.452][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-07 13:19:09.546][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:09.548][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-03-07 13:19:09.552][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-03-07 13:19:09.557][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-07 13:19:09.560][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:09.561][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:09.563][private$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[2025-03-07 13:19:09.660][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[2025-03-07 13:19:09.758][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:09.760][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-03-07 13:19:09.765][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-03-07 13:19:09.768][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:09.769][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:09.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:09.776][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:09.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:09.778][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:09.779][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.TRACE[2025-03-07 13:19:09.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:09.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:09.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:09.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:09.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:09.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:09.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:09.791][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:09.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:09.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:09.799][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:09.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:09.801][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:09.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:09.803][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:09.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:09.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:09.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:09.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:09.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:09.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:09.814][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:09.814][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:09.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:09.821][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:09.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:09.822][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:09.823][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.TRACE[2025-03-07 13:19:09.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:09.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:09.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.827][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:09.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:09.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:09.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:09.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:09.858][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-07 13:19:09.882][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:09.883][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:09.884][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:09.890][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:09.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:09.892][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:09.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:09.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.902][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:09.902][private$selectFields]
biodb.TRACE[2025-03-07 13:19:09.903][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 13:19:09.904][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 13:19:09.905][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:09.906][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.907][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.907][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.908][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.909][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.910][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.911][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.911][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.912][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:09.913][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:09.914][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.915][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.915][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.916][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.917][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 13:19:09.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.928][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-07 13:19:09.929][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:09.930][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:09.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:09.936][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:09.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:09.937][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:09.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:09.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.955][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.978][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:09.979][private$selectFields]
biodb.TRACE[2025-03-07 13:19:09.980][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 13:19:09.981][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 13:19:09.982][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:09.982][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.983][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.984][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.985][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.986][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.986][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:09.987][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:09.988][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:09.989][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:09.999][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.000][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.001][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.003][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.003][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 13:19:10.004][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.008][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.024][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.028][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-07 13:19:10.029][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:10.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:10.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:10.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:10.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:10.037][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:10.038][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[2025-03-07 13:19:10.039][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.043][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.046][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.047][private$selectFields]
biodb.TRACE[2025-03-07 13:19:10.047][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 13:19:10.048][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 13:19:10.049][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.050][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.050][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.052][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.053][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.054][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.054][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.055][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.056][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.057][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.057][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.058][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.060][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.061][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 13:19:10.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.065][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.068][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.071][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-07 13:19:10.072][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-07 13:19:10.073][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-07 13:19:10.082][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-07 13:19:10.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-07 13:19:10.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-07 13:19:10.089][biodb::testThat]
biodb.INFO [2025-03-07 13:19:10.090][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-03-07 13:19:10.092][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 13:19:10.093][biodb::testThat]
biodb.TRACE[2025-03-07 13:19:10.096][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-07 13:19:10.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-07 13:19:10.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.100][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.104][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.107][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.110][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:10.116][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:10.117][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:10.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:10.124][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:10.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:10.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:10.126][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[2025-03-07 13:19:10.129][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[2025-03-07 13:19:10.133][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 13:19:10.134][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-07 13:19:10.135][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 13:19:10.137][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-07 13:19:10.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:10.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:10.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:10.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:10.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:10.148][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:10.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:10.150][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.157][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:10.161][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[2025-03-07 13:19:10.165][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 13:19:10.167][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-07 13:19:10.168][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 13:19:10.169][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-07 13:19:10.172][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:10.173][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:10.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:10.179][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:10.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:10.181][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:10.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:10.183][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.187][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.190][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:10.194][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:10.194][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:10.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:10.201][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:10.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:10.203][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:10.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:10.205][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.208][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:10.216][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-07 13:19:10.218][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:10.219][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:10.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:10.226][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:10.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:10.227][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:10.228][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.TRACE[2025-03-07 13:19:10.229][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.236][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.237][private$selectFields]
biodb.TRACE[2025-03-07 13:19:10.238][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 13:19:10.238][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 13:19:10.239][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.240][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.241][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.242][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.242][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.243][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.244][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.245][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.246][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.247][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.248][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.249][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.249][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.250][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.251][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 13:19:10.252][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.255][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.258][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.262][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-07 13:19:10.263][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:10.264][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:10.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:10.270][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:10.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:10.272][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:10.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:10.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.281][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.281][private$selectFields]
biodb.TRACE[2025-03-07 13:19:10.282][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 13:19:10.283][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 13:19:10.284][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.284][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.285][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.286][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.287][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.288][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.288][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.289][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.290][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.291][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.292][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.292][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.293][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.294][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.295][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.295][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 13:19:10.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.300][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.303][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.306][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-07 13:19:10.308][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:10.308][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:10.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:10.314][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:10.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:10.316][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:10.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:10.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.322][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.325][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.325][private$selectFields]
biodb.TRACE[2025-03-07 13:19:10.326][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 13:19:10.327][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 13:19:10.328][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.329][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.330][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.330][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.331][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.332][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.333][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.334][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.335][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.336][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.337][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.338][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.338][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.339][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.340][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 13:19:10.341][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.355][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.359][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-07 13:19:10.360][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-07 13:19:10.361][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-07 13:19:10.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.378][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.381][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:10.387][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:10.388][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:10.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:10.394][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:10.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:10.396][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:10.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:10.400][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[2025-03-07 13:19:10.403][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 13:19:10.404][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-07 13:19:10.406][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 13:19:10.407][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-07 13:19:10.411][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[2025-03-07 13:19:10.414][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 13:19:10.415][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-07 13:19:10.416][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 13:19:10.418][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-07 13:19:10.420][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:10.421][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:10.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:10.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:10.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:10.429][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:10.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:10.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.434][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:10.440][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:10.441][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:10.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:10.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:10.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:10.449][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:10.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:10.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.458][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:10.461][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:10.462][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:10.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:10.468][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:10.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:10.470][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:10.471][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[2025-03-07 13:19:10.472][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.475][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:10.482][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-07 13:19:10.483][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:10.484][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:10.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:10.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:10.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:10.492][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:10.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:10.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.500][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.501][private$selectFields]
biodb.TRACE[2025-03-07 13:19:10.502][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 13:19:10.502][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 13:19:10.503][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.504][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.505][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.506][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.506][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.507][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.508][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.509][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.510][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.510][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.511][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.512][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.513][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.513][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.514][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.515][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 13:19:10.516][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.526][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-07 13:19:10.527][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:10.527][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:10.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:10.533][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:10.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:10.535][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:10.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:10.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.540][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.544][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.544][private$selectFields]
biodb.TRACE[2025-03-07 13:19:10.545][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 13:19:10.546][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 13:19:10.547][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.548][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.548][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.549][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.550][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.551][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.552][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.553][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.554][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.555][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.555][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.556][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.557][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.558][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.559][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 13:19:10.560][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.563][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.570][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-07 13:19:10.571][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:10.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:10.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:10.578][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:10.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:10.579][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:10.580][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[2025-03-07 13:19:10.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.585][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.588][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.589][private$selectFields]
biodb.TRACE[2025-03-07 13:19:10.589][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 13:19:10.590][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 13:19:10.591][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.592][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.593][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.594][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.595][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.596][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.596][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.597][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.598][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.599][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.600][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.600][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.601][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.602][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.603][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 13:19:10.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.607][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.614][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-07 13:19:10.614][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-07 13:19:10.615][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-07 13:19:10.624][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-07 13:19:10.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-07 13:19:10.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-07 13:19:10.632][biodb::testThat]
biodb.INFO [2025-03-07 13:19:10.633][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-03-07 13:19:10.634][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 13:19:10.635][biodb::testThat]
biodb.TRACE[2025-03-07 13:19:10.638][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-07 13:19:10.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-07 13:19:10.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.641][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.648][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.651][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:10.659][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:10.660][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:10.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:10.666][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:10.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:10.667][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:10.668][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[2025-03-07 13:19:10.671][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[2025-03-07 13:19:10.674][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 13:19:10.676][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-07 13:19:10.677][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 13:19:10.685][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-07 13:19:10.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:10.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:10.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:10.695][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:10.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:10.697][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:10.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:10.698][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.705][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:10.709][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[2025-03-07 13:19:10.712][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 13:19:10.714][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-07 13:19:10.715][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 13:19:10.716][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-07 13:19:10.719][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:10.719][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:10.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:10.726][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:10.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:10.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:10.729][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.TRACE[2025-03-07 13:19:10.730][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.734][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.737][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:10.741][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:10.742][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:10.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:10.748][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:10.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:10.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:10.751][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.TRACE[2025-03-07 13:19:10.752][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.756][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.759][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:10.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:10.763][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-07 13:19:10.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:10.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:10.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:10.773][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:10.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:10.775][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:10.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:10.777][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.781][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.784][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.785][private$selectFields]
biodb.TRACE[2025-03-07 13:19:10.786][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 13:19:10.787][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 13:19:10.787][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.788][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.789][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.791][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.792][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.793][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.794][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.795][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.795][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.796][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.797][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.798][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.799][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.799][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.800][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 13:19:10.801][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.811][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-07 13:19:10.812][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:10.813][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:10.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:10.819][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:10.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:10.821][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:10.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:10.823][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.826][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.829][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.831][private$selectFields]
biodb.TRACE[2025-03-07 13:19:10.832][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 13:19:10.833][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 13:19:10.834][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.834][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.835][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.837][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.838][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.839][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.839][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.840][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.841][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.842][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.843][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.843][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.844][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.845][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.846][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 13:19:10.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.850][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.857][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-07 13:19:10.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:10.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:10.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:10.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:10.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:10.866][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:10.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:10.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.875][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.876][private$selectFields]
biodb.TRACE[2025-03-07 13:19:10.876][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 13:19:10.877][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 13:19:10.878][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.879][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.880][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.880][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.881][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.882][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.883][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.883][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.884][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.885][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.886][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:10.887][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.887][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.888][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.889][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.890][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 13:19:10.891][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.895][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.899][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:10.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.903][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-07 13:19:10.904][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-07 13:19:10.905][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-07 13:19:10.927][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.931][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.934][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:10.938][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:10.946][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:10.947][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:10.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:10.953][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:10.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:10.955][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:10.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:10.959][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[2025-03-07 13:19:10.963][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 13:19:10.964][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-07 13:19:10.965][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 13:19:10.967][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-07 13:19:10.971][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[2025-03-07 13:19:10.974][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 13:19:10.975][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-07 13:19:10.977][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 13:19:10.978][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-07 13:19:10.982][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:10.983][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:10.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:10.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:10.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:10.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:10.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:10.996][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:10.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:10.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:11.006][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:11.007][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:11.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:11.013][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:11.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:11.015][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:11.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:11.017][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.024][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:11.028][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:11.036][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:11.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:11.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:11.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:11.045][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:11.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:11.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.050][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.053][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:11.057][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-07 13:19:11.058][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:11.059][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:11.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:11.065][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:11.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:11.067][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:11.068][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.TRACE[2025-03-07 13:19:11.069][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.072][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.075][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:11.076][private$selectFields]
biodb.TRACE[2025-03-07 13:19:11.077][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 13:19:11.078][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 13:19:11.078][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:11.079][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.080][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.082][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.082][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.083][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.085][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.086][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:11.086][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:11.087][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.088][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.089][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.089][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.090][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 13:19:11.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.094][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.098][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.101][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-07 13:19:11.102][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:11.103][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:11.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:11.109][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:11.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:11.111][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:11.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:11.113][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.116][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.120][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:11.121][private$selectFields]
biodb.TRACE[2025-03-07 13:19:11.121][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 13:19:11.122][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 13:19:11.123][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:11.124][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.125][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.127][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.128][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.129][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.130][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.131][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:11.132][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:11.133][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.134][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.135][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.136][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 13:19:11.137][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.140][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.144][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.147][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-07 13:19:11.148][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:11.149][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:11.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:11.155][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:11.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:11.157][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:11.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:11.159][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.162][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.166][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:11.166][private$selectFields]
biodb.TRACE[2025-03-07 13:19:11.167][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-07 13:19:11.168][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-07 13:19:11.169][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:11.170][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.171][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.171][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.172][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.173][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.174][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.175][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.176][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:11.177][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-07 13:19:11.178][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.179][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.180][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.180][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.181][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-07 13:19:11.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.186][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.189][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.193][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-07 13:19:11.194][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-07 13:19:11.194][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-07 13:19:11.217][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-07 13:19:11.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-07 13:19:11.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-07 13:19:11.227][biodb::testThat]
biodb.INFO [2025-03-07 13:19:11.228][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2025-03-07 13:19:11.230][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 13:19:11.231][biodb::testThat]
biodb.DEBUG[2025-03-07 13:19:11.233][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-03-07 13:19:11.234][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 13:19:11.236][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-03-07 13:19:11.239][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 13:19:11.240][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 13:19:11.242][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:19:11.243][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:19:11.244][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 13:19:11.245][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 13:19:11.248][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:11.249][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:11.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:11.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:11.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:11.258][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:11.259][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[2025-03-07 13:19:11.260][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-03-07 13:19:11.263][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:11.264][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:11.266][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-03-07 13:19:11.382][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-03-07 13:19:11.479][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:11.482][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-03-07 13:19:11.486][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-03-07 13:19:11.488][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-03-07 13:19:11.490][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 13:19:11.491][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:19:11.492][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:19:11.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:11.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:11.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:11.501][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:11.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:11.502][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:11.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:11.505][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.507][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.507][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.508][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.513][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:11.514][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:11.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.515][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.516][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:11.518][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:11.519][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.520][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.521][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:11.523][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:11.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.524][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.525][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:11.526][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:11.527][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.528][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.529][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:11.530][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:11.531][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.532][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.533][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:11.534][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:11.534][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.535][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.536][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.537][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.538][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.539][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.540][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:11.541][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:11.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.543][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.544][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:11.545][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:11.546][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.547][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.548][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:11.549][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:11.549][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.550][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.551][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.561][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:11.597][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-03-07 13:19:11.597][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-03-07 13:19:11.606][biodb::testThat]
biodb.INFO [2025-03-07 13:19:11.607][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-03-07 13:19:11.608][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 13:19:11.609][biodb::testThat]
biodb.DEBUG[2025-03-07 13:19:11.620][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-03-07 13:19:11.621][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-03-07 13:19:11.623][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-03-07 13:19:11.624][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-03-07 13:19:11.627][cch$loadFileContent] file.exist = [3]: "TRUE, TRUE, TRUE".
biodb.TRACE[2025-03-07 13:19:11.630][loadFileContents] Loaded 3 files from cache: [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml".
biodb.DEBUG[2025-03-07 13:19:11.631][conn$getEntryContent] 3 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:19:11.632][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-03-07 13:19:11.634][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-03-07 13:19:11.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:11.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:11.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:11.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:11.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:11.645][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:11.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:11.648][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.649][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.650][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.650][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.654][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:11.655][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:11.655][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.656][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.657][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:11.658][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:11.658][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.659][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.660][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:11.661][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:11.661][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.662][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.662][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:11.663][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:11.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.664][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.665][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:11.665][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:11.666][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.667][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.667][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:11.668][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:11.668][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.669][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.669][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.670][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.670][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.671][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.672][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:11.672][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:11.672][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.673][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.674][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:11.674][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:11.674][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.675][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.676][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:11.676][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:11.677][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.677][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.680][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:11.691][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:11.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:11.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:11.695][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:11.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:11.696][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:11.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:11.698][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.698][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.698][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.699][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.701][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:11.702][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:11.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.702][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.703][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:11.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:11.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.704][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:11.705][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:11.705][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.705][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.706][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:11.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:11.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.707][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:11.708][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:11.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.708][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.709][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:11.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:11.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.710][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:11.711][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:11.711][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.711][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.712][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:11.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:11.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.714][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:11.714][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:11.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.715][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.715][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:11.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:11.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.717][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:11.717][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:11.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.718][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.718][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:11.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:11.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.720][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.720][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.720][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.721][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.721][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.723][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:11.723][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:11.724][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.724][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.724][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:11.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:11.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.726][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:11.726][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:11.727][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.727][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.727][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:11.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:11.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.729][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:11.729][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:11.729][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.730][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.730][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:11.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:11.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.732][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.735][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:11.741][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:11.741][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:11.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:11.744][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:11.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:11.745][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:11.746][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[2025-03-07 13:19:11.747][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.748][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.750][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.751][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.756][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:11.756][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:11.756][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.758][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.759][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:11.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:11.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.763][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:11.764][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:11.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.766][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.767][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:11.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:11.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.770][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:11.771][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:11.772][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.773][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:11.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:11.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.777][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:11.778][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:11.779][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.780][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.781][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:11.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:11.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.783][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:11.783][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:11.784][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.784][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.785][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:11.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:11.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.786][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:11.786][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:11.787][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.787][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.787][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:11.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:11.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.789][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.789][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.789][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.790][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:11.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.792][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:11.792][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:11.792][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.793][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.793][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:11.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:11.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.798][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:11.799][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:11.800][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.800][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.802][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:11.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:11.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.813][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:11.813][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:11.814][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.815][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.816][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:11.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:11.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.820][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.823][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.831][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:11.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:11.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:11.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:11.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:11.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:11.873][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-03-07 13:19:11.873][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-03-07 13:19:11.874][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-03-07 13:19:11.884][biodb::testThat]
biodb.INFO [2025-03-07 13:19:11.885][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2025-03-07 13:19:11.885][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 13:19:11.885][biodb::testThat]
biodb.INFO [2025-03-07 13:19:11.902][biodb::testThat]
biodb.INFO [2025-03-07 13:19:11.903][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2025-03-07 13:19:11.903][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 13:19:11.904][biodb::testThat]
biodb.INFO [2025-03-07 13:19:11.912][biodb::testThat]
biodb.INFO [2025-03-07 13:19:11.913][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2025-03-07 13:19:11.914][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 13:19:11.915][biodb::testThat]
biodb.DEBUG[2025-03-07 13:19:11.917][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.INFO [2025-03-07 13:19:11.920][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2025-03-07 13:19:11.921][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:11.922][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:11.924][private$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[2025-03-07 13:19:12.111][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[2025-03-07 13:19:12.287][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:12.289][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-03-07 13:19:12.291][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-03-07 13:19:12.299][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:12.299][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:12.300][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:12.300][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:12.300][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:12.301][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:12.301][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:12.301][ef$get] fields variable is a list.
biodb.INFO [2025-03-07 13:19:12.302][biodb::testThat]
biodb.INFO [2025-03-07 13:19:12.303][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2025-03-07 13:19:12.303][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 13:19:12.303][biodb::testThat]
biodb.ERROR[2025-03-07 13:19:12.311][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-03-07 13:19:12.321][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-03-07 13:19:12.329][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-07 13:19:12.330][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-07 13:19:12.331][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-07 13:19:12.331][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-07 13:19:12.331][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:12.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:12.332][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.333][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-07 13:19:12.338][biodb::testContext]
biodb.INFO [2025-03-07 13:19:12.339][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-07 13:19:12.339][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-03-07 13:19:12.340][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-07 13:19:12.340][biodb::testContext]
biodb.INFO [2025-03-07 13:19:12.341][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-07 13:19:12.342][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-07 13:19:12.344][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 13:19:12.344][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-07 13:19:12.345][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-07 13:19:12.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.346][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-07 13:19:12.347][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-07 13:19:12.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.348][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-07 13:19:12.348][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-07 13:19:12.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.349][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-07 13:19:12.350][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-07 13:19:12.350][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-07 13:19:12.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.351][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-07 13:19:12.352][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-07 13:19:12.352][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-07 13:19:12.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.353][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-07 13:19:12.353][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-07 13:19:12.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.354][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[2025-03-07 13:19:12.355][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-07 13:19:12.355][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-07 13:19:12.355][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-07 13:19:12.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.356][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-07 13:19:12.357][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-07 13:19:12.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.358][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[2025-03-07 13:19:12.358][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-07 13:19:12.358][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-07 13:19:12.359][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-07 13:19:12.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.360][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-07 13:19:12.360][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-07 13:19:12.361][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-07 13:19:12.361][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-07 13:19:12.361][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-07 13:19:12.362][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-07 13:19:12.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.363][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[2025-03-07 13:19:12.363][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-07 13:19:12.363][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-07 13:19:12.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.365][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-07 13:19:12.365][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-07 13:19:12.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.367][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-07 13:19:12.367][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-07 13:19:12.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.368][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-07 13:19:12.368][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-07 13:19:12.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.370][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-07 13:19:12.370][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-07 13:19:12.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.371][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-07 13:19:12.371][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-07 13:19:12.387][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-07 13:19:12.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.388][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[2025-03-07 13:19:12.389][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-07 13:19:12.389][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-07 13:19:12.390][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-07 13:19:12.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.391][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-07 13:19:12.392][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:12.392][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-07 13:19:12.393][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:12.393][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 13:19:12.393][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:12.403][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 13:19:12.404][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:12.405][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 13:19:12.405][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-07 13:19:12.406][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 13:19:12.406][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:12.406][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-07 13:19:12.407][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 13:19:12.407][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:12.407][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:12.408][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 13:19:12.408][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 13:19:12.408][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 13:19:12.408][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-07 13:19:12.408][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-07 13:19:12.408][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 13:19:12.408][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:12.409][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:12.409][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 13:19:12.409][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:12.410][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:12.410][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 13:19:12.411][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:12.411][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 13:19:12.411][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 13:19:12.411][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:12.412][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:12.412][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-07 13:19:12.413][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:12.413][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-07 13:19:12.414][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:12.414][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 13:19:12.414][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:12.415][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 13:19:12.415][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:12.415][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 13:19:12.416][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-07 13:19:12.416][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 13:19:12.417][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:12.417][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-07 13:19:12.418][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 13:19:12.418][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:12.418][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:12.419][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 13:19:12.419][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 13:19:12.419][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 13:19:12.419][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-07 13:19:12.419][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-07 13:19:12.419][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 13:19:12.419][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:12.420][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:12.420][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 13:19:12.420][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:12.421][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:12.421][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 13:19:12.421][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:12.422][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 13:19:12.422][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 13:19:12.422][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:12.423][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:12.423][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-07 13:19:12.424][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:12.424][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-07 13:19:12.425][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:12.425][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 13:19:12.425][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:12.426][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 13:19:12.426][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:12.427][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 13:19:12.427][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-07 13:19:12.427][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 13:19:12.428][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:12.428][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-07 13:19:12.428][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 13:19:12.429][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:12.429][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:12.429][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:12.430][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 13:19:12.430][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:12.430][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:12.431][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 13:19:12.431][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:12.431][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:12.432][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 13:19:12.432][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:12.432][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 13:19:12.432][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 13:19:12.433][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:12.433][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:12.433][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-07 13:19:12.434][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:12.435][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-07 13:19:12.435][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:12.435][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 13:19:12.436][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:12.436][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 13:19:12.437][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:12.437][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 13:19:12.437][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-07 13:19:12.438][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 13:19:12.438][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:12.438][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-07 13:19:12.439][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 13:19:12.439][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:12.440][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:12.440][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:12.440][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 13:19:12.441][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:12.441][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:12.441][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 13:19:12.442][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:12.442][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:12.442][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 13:19:12.443][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:12.443][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 13:19:12.443][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 13:19:12.444][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:12.444][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:12.445][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 13:19:12.445][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.449][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[2025-03-07 13:19:12.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.461][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[2025-03-07 13:19:12.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.472][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-07 13:19:12.473][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-07 13:19:12.473][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-07 13:19:12.474][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-07 13:19:12.474][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-07 13:19:12.475][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-07 13:19:12.475][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-07 13:19:12.476][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-07 13:19:12.476][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-07 13:19:12.477][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-07 13:19:12.477][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-07 13:19:12.478][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-07 13:19:12.478][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-07 13:19:12.479][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-07 13:19:12.479][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-07 13:19:12.480][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-07 13:19:12.480][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-07 13:19:12.481][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-07 13:19:12.481][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-07 13:19:12.482][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-07 13:19:12.482][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-07 13:19:12.483][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-07 13:19:12.484][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-07 13:19:12.484][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-07 13:19:12.485][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-07 13:19:12.485][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-07 13:19:12.486][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-07 13:19:12.486][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-07 13:19:12.487][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-07 13:19:12.487][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-07 13:19:12.488][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-07 13:19:12.488][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-07 13:19:12.489][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-07 13:19:12.489][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-07 13:19:12.490][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-07 13:19:12.490][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-07 13:19:12.491][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-07 13:19:12.491][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-07 13:19:12.492][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-07 13:19:12.492][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-07 13:19:12.493][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-07 13:19:12.493][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-07 13:19:12.494][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-07 13:19:12.494][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-07 13:19:12.496][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-07 13:19:12.497][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-07 13:19:12.498][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-07 13:19:12.499][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-07 13:19:12.499][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-07 13:19:12.500][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-07 13:19:12.500][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-07 13:19:12.501][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-07 13:19:12.501][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-07 13:19:12.502][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-07 13:19:12.502][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-07 13:19:12.503][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-07 13:19:12.503][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-07 13:19:12.504][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-07 13:19:12.504][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-07 13:19:12.505][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-07 13:19:12.505][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-07 13:19:12.506][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-07 13:19:12.506][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-07 13:19:12.507][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-07 13:19:12.507][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-07 13:19:12.508][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-07 13:19:12.508][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-07 13:19:12.509][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-07 13:19:12.509][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-07 13:19:12.510][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-07 13:19:12.510][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-07 13:19:12.511][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-07 13:19:12.511][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-07 13:19:12.512][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-07 13:19:12.513][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-07 13:19:12.513][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-07 13:19:12.514][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-07 13:19:12.514][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-07 13:19:12.515][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-07 13:19:12.515][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-07 13:19:12.516][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-07 13:19:12.516][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-07 13:19:12.517][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-07 13:19:12.517][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-07 13:19:12.518][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-07 13:19:12.519][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 13:19:12.519][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.520][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.520][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[2025-03-07 13:19:12.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:12.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:12.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:12.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:12.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:12.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:12.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:12.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:12.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:12.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:12.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.539][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[2025-03-07 13:19:12.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:12.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:12.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:12.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:12.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.543][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[2025-03-07 13:19:12.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:12.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:12.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:12.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:12.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:12.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:12.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:12.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:12.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:12.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:12.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:12.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:12.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:12.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:12.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:12.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:12.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:12.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:12.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:12.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:12.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:12.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:12.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:12.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:12.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:12.567][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-07 13:19:12.568][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-07 13:19:12.569][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:12.570][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-07 13:19:12.570][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:12.571][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 13:19:12.571][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:12.571][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 13:19:12.572][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:12.572][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-07 13:19:12.573][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-07 13:19:12.573][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 13:19:12.574][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:12.574][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-07 13:19:12.574][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 13:19:12.575][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-07 13:19:12.575][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-07 13:19:12.575][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-07 13:19:12.575][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-07 13:19:12.575][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-07 13:19:12.575][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-07 13:19:12.575][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-07 13:19:12.575][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-07 13:19:12.575][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-07 13:19:12.575][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-07 13:19:12.575][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-07 13:19:12.575][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:12.575][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 13:19:12.575][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 13:19:12.575][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 13:19:12.576][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-07 13:19:12.576][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:12.577][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:12.577][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 13:19:12.577][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:12.578][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:12.578][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 13:19:12.578][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:19:12.578][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-07 13:19:12.579][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 13:19:12.579][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 13:19:12.579][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:12.580][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-07 13:19:12.580][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-07 13:19:12.580][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-07 13:19:12.581][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-07 13:19:12.582][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-07 13:19:12.582][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-07 13:19:12.583][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-07 13:19:12.583][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-07 13:19:12.585][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-07 13:19:12.586][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-07 13:19:12.586][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-07 13:19:12.587][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-07 13:19:12.587][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-07 13:19:12.588][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-07 13:19:12.588][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-07 13:19:12.589][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-07 13:19:12.589][biodb::testThat]
biodb.INFO [2025-03-07 13:19:12.590][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2025-03-07 13:19:12.590][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 13:19:12.590][biodb::testThat]
biodb.DEBUG[2025-03-07 13:19:12.592][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-07 13:19:12.595][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:12.595][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:12.596][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-03-07 13:19:12.670][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-03-07 13:19:12.774][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:12.776][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-03-07 13:19:12.780][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-03-07 13:19:12.784][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 13:19:12.787][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:12.788][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:12.790][private$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[2025-03-07 13:19:12.900][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[2025-03-07 13:19:13.007][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:13.010][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-03-07 13:19:13.015][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-03-07 13:19:13.017][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:13.018][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:13.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:13.025][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:13.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:13.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:13.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:13.029][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[2025-03-07 13:19:13.033][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:13.034][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:13.035][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-07 13:19:13.133][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-07 13:19:13.235][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:13.238][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-03-07 13:19:13.242][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-03-07 13:19:13.245][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:13.246][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:13.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:13.253][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:13.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:13.254][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:13.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:13.272][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:13.273][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:13.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:13.280][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:13.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:13.282][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:13.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:13.288][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 13:19:13.291][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 13:19:13.293][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-07 13:19:13.294][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 13:19:13.296][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-07 13:19:13.298][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:13.299][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:13.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:13.305][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:13.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:13.307][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:13.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:13.309][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 13:19:13.313][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 13:19:13.315][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-07 13:19:13.316][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 13:19:13.318][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-07 13:19:13.321][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:13.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:13.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:13.327][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:13.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:13.329][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:13.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:13.331][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:13.332][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:13.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:13.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:13.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:13.339][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:13.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:13.344][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 13:19:13.347][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 13:19:13.348][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-07 13:19:13.350][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 13:19:13.351][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-07 13:19:13.353][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:13.354][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:13.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:13.360][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:13.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:13.362][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:13.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:13.365][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 13:19:13.368][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 13:19:13.369][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-07 13:19:13.371][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 13:19:13.372][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-07 13:19:13.374][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:13.374][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:13.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:13.382][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:13.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:13.383][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:13.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:13.386][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 13:19:13.406][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:13.407][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2025-03-07 13:19:13.409][rule$waitAsNeeded] Wait 0.187363 second(s).
biodb.TRACE[2025-03-07 13:19:13.749][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-07 13:19:13.855][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-07 13:19:13.968][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:13.971][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-03-07 13:19:13.976][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-03-07 13:19:13.979][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:13.980][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:13.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:13.986][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:13.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:13.988][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:13.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-07 13:19:13.995][biodb::testThat]
biodb.INFO [2025-03-07 13:19:13.996][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2025-03-07 13:19:13.997][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 13:19:13.998][biodb::testThat]
biodb.DEBUG[2025-03-07 13:19:14.001][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 13:19:14.005][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:14.006][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:14.008][private$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[2025-03-07 13:19:14.109][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[2025-03-07 13:19:14.204][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2025-03-07 13:19:14.208][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-03-07 13:19:14.210][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-03-07 13:19:14.215][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-03-07 13:19:14.217][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:14.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:14.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:14.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.227][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.233][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 13:19:14.236][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:14.237][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:14.239][private$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[2025-03-07 13:19:14.342][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[2025-03-07 13:19:14.446][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:14.449][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-03-07 13:19:14.453][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-03-07 13:19:14.457][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:14.458][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:14.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:14.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.466][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.466][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.INFO [2025-03-07 13:19:14.472][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-07 13:19:14.473][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-07 13:19:14.474][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-07 13:19:14.475][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-07 13:19:14.476][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:14.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:14.478][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.480][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-07 13:19:14.486][biodb::testContext]
biodb.INFO [2025-03-07 13:19:14.487][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-07 13:19:14.488][biodb::testContext] Test context - Test web services
biodb.INFO [2025-03-07 13:19:14.489][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-07 13:19:14.489][biodb::testContext]
biodb.INFO [2025-03-07 13:19:14.492][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-07 13:19:14.493][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-07 13:19:14.499][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 13:19:14.500][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-07 13:19:14.501][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-07 13:19:14.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.505][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-07 13:19:14.505][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-07 13:19:14.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.508][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-07 13:19:14.509][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-07 13:19:14.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.513][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-07 13:19:14.514][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-07 13:19:14.515][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-07 13:19:14.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.517][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-07 13:19:14.519][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-07 13:19:14.520][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-07 13:19:14.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.524][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-07 13:19:14.525][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-07 13:19:14.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.528][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-07 13:19:14.528][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-07 13:19:14.529][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-07 13:19:14.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.532][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-07 13:19:14.533][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-07 13:19:14.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.536][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-07 13:19:14.537][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-07 13:19:14.538][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-07 13:19:14.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.541][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-07 13:19:14.541][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-07 13:19:14.542][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-07 13:19:14.543][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-07 13:19:14.544][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-07 13:19:14.545][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-07 13:19:14.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.547][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[2025-03-07 13:19:14.548][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-07 13:19:14.548][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-07 13:19:14.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.551][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-07 13:19:14.552][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-07 13:19:14.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.554][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[2025-03-07 13:19:14.555][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-07 13:19:14.556][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-07 13:19:14.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.559][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-07 13:19:14.560][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-07 13:19:14.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.562][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[2025-03-07 13:19:14.563][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-07 13:19:14.564][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-07 13:19:14.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.567][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-07 13:19:14.567][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-07 13:19:14.585][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-07 13:19:14.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.588][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[2025-03-07 13:19:14.589][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-07 13:19:14.589][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-07 13:19:14.590][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-07 13:19:14.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.594][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-07 13:19:14.595][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:14.596][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-07 13:19:14.597][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:14.598][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 13:19:14.599][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:14.600][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 13:19:14.601][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:14.601][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 13:19:14.602][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-07 13:19:14.603][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 13:19:14.604][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:14.605][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-07 13:19:14.606][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 13:19:14.606][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:14.607][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:14.608][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 13:19:14.608][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 13:19:14.608][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 13:19:14.608][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-07 13:19:14.608][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-07 13:19:14.609][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 13:19:14.610][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:14.610][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:14.611][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 13:19:14.612][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:14.613][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:14.613][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 13:19:14.614][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:14.615][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 13:19:14.616][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 13:19:14.617][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:14.617][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:14.618][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-07 13:19:14.620][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:14.621][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-07 13:19:14.622][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:14.623][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 13:19:14.623][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:14.624][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 13:19:14.625][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:14.626][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 13:19:14.627][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-07 13:19:14.627][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 13:19:14.629][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:14.629][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-07 13:19:14.630][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 13:19:14.631][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:14.632][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:14.633][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 13:19:14.633][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 13:19:14.633][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 13:19:14.633][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-07 13:19:14.633][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-07 13:19:14.634][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 13:19:14.634][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:14.635][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:14.636][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 13:19:14.637][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:14.638][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:14.638][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 13:19:14.639][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:14.640][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 13:19:14.641][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 13:19:14.642][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:14.642][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:14.643][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-07 13:19:14.646][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:14.647][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-07 13:19:14.648][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:14.649][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 13:19:14.649][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:14.650][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 13:19:14.651][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:14.652][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 13:19:14.653][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-07 13:19:14.654][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 13:19:14.654][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:14.655][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-07 13:19:14.656][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 13:19:14.657][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:14.658][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:14.659][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:14.659][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 13:19:14.660][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:14.661][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:14.662][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 13:19:14.662][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:14.663][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:14.664][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 13:19:14.665][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:14.666][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 13:19:14.667][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 13:19:14.668][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:14.669][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:14.670][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-07 13:19:14.672][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:14.673][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-07 13:19:14.673][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:14.674][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 13:19:14.675][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:14.676][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 13:19:14.677][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:14.677][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 13:19:14.678][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-07 13:19:14.679][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 13:19:14.680][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:14.681][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-07 13:19:14.682][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 13:19:14.683][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:14.684][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:14.684][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:14.685][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 13:19:14.686][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:14.687][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:14.688][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 13:19:14.688][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:14.689][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:14.690][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 13:19:14.691][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:14.691][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 13:19:14.692][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 13:19:14.693][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:14.694][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:14.695][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 13:19:14.696][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.730][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[2025-03-07 13:19:14.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.759][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[2025-03-07 13:19:14.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.766][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[2025-03-07 13:19:14.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.777][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[2025-03-07 13:19:14.778][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-07 13:19:14.779][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-07 13:19:14.780][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-07 13:19:14.781][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-07 13:19:14.783][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-07 13:19:14.784][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-07 13:19:14.785][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-07 13:19:14.787][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-07 13:19:14.788][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-07 13:19:14.789][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-07 13:19:14.790][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-07 13:19:14.791][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-07 13:19:14.793][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-07 13:19:14.794][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-07 13:19:14.795][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-07 13:19:14.796][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-07 13:19:14.797][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-07 13:19:14.799][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-07 13:19:14.800][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-07 13:19:14.801][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-07 13:19:14.802][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-07 13:19:14.803][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-07 13:19:14.805][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-07 13:19:14.806][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-07 13:19:14.807][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-07 13:19:14.808][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-07 13:19:14.809][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-07 13:19:14.811][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-07 13:19:14.812][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-07 13:19:14.813][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-07 13:19:14.814][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-07 13:19:14.815][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-07 13:19:14.816][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-07 13:19:14.818][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-07 13:19:14.819][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-07 13:19:14.820][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-07 13:19:14.821][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-07 13:19:14.822][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-07 13:19:14.823][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-07 13:19:14.825][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-07 13:19:14.826][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-07 13:19:14.827][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-07 13:19:14.828][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-07 13:19:14.829][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-07 13:19:14.830][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-07 13:19:14.832][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-07 13:19:14.833][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-07 13:19:14.834][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-07 13:19:14.835][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-07 13:19:14.836][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-07 13:19:14.838][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-07 13:19:14.839][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-07 13:19:14.840][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-07 13:19:14.841][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-07 13:19:14.843][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-07 13:19:14.844][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-07 13:19:14.845][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-07 13:19:14.846][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-07 13:19:14.847][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-07 13:19:14.848][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-07 13:19:14.849][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-07 13:19:14.851][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-07 13:19:14.852][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-07 13:19:14.853][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-07 13:19:14.854][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-07 13:19:14.855][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-07 13:19:14.856][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-07 13:19:14.858][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-07 13:19:14.859][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-07 13:19:14.860][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-07 13:19:14.861][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-07 13:19:14.862][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-07 13:19:14.863][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-07 13:19:14.864][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-07 13:19:14.866][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-07 13:19:14.868][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-07 13:19:14.869][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-07 13:19:14.871][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-07 13:19:14.872][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-07 13:19:14.873][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-07 13:19:14.875][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-07 13:19:14.876][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-07 13:19:14.877][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-07 13:19:14.878][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-07 13:19:14.880][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-07 13:19:14.881][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 13:19:14.882][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.883][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:14.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:14.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:14.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:14.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:14.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:14.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:14.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:14.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:14.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:14.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.913][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[2025-03-07 13:19:14.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:14.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:14.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:14.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:14.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:14.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:14.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.929][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.DEBUG[2025-03-07 13:19:14.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:14.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:14.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:14.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:14.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.939][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.DEBUG[2025-03-07 13:19:14.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:14.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:14.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.945][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[2025-03-07 13:19:14.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:14.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:14.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:14.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:14.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:14.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:14.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:14.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:14.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.968][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[2025-03-07 13:19:14.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:14.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:14.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:14.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:14.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:14.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:14.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:14.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:14.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:14.978][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.DEBUG[2025-03-07 13:19:14.980][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-07 13:19:14.982][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-07 13:19:14.984][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:14.984][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-07 13:19:14.985][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:14.986][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 13:19:14.987][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:14.988][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 13:19:14.989][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:14.990][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-07 13:19:14.991][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-07 13:19:14.992][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 13:19:14.993][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:14.994][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-07 13:19:14.995][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 13:19:14.996][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-07 13:19:14.996][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-07 13:19:14.996][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-07 13:19:14.996][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-07 13:19:14.996][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-07 13:19:14.996][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-07 13:19:14.996][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-07 13:19:14.996][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-07 13:19:14.996][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-07 13:19:14.996][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-07 13:19:14.996][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-07 13:19:14.997][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:14.997][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 13:19:14.997][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 13:19:14.997][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 13:19:14.998][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-07 13:19:14.999][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:15.000][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:15.001][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 13:19:15.002][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:15.002][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:15.011][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 13:19:15.012][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:19:15.012][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-07 13:19:15.013][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 13:19:15.014][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 13:19:15.014][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:15.015][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-07 13:19:15.015][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-07 13:19:15.016][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-07 13:19:15.018][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-07 13:19:15.020][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-07 13:19:15.021][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-07 13:19:15.023][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-07 13:19:15.024][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-07 13:19:15.028][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-07 13:19:15.029][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-07 13:19:15.030][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-07 13:19:15.031][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-07 13:19:15.032][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-07 13:19:15.033][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-07 13:19:15.034][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-07 13:19:15.035][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-07 13:19:15.036][biodb::testThat]
biodb.INFO [2025-03-07 13:19:15.037][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-03-07 13:19:15.038][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 13:19:15.039][biodb::testThat]
biodb.DEBUG[2025-03-07 13:19:15.042][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-07 13:19:15.046][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:15.047][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:15.048][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-03-07 13:19:15.135][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-03-07 13:19:15.227][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:15.229][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-03-07 13:19:15.233][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-03-07 13:19:15.238][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-07 13:19:15.242][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:15.243][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:15.245][private$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[2025-03-07 13:19:15.352][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[2025-03-07 13:19:15.450][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:15.453][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-03-07 13:19:15.458][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-03-07 13:19:15.467][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-07 13:19:15.469][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-07 13:19:15.470][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-07 13:19:15.471][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-07 13:19:15.471][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:15.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:15.473][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.474][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.475][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.INFO [2025-03-07 13:19:15.480][biodb::testContext]
biodb.INFO [2025-03-07 13:19:15.481][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-07 13:19:15.482][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-03-07 13:19:15.483][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-07 13:19:15.484][biodb::testContext]
biodb.INFO [2025-03-07 13:19:15.486][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-07 13:19:15.488][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-07 13:19:15.493][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 13:19:15.494][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-07 13:19:15.495][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-07 13:19:15.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.498][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-07 13:19:15.499][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-07 13:19:15.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.502][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-07 13:19:15.503][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-07 13:19:15.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.506][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-07 13:19:15.507][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-07 13:19:15.508][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-07 13:19:15.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.512][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-07 13:19:15.513][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-07 13:19:15.514][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-07 13:19:15.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.517][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-07 13:19:15.518][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-07 13:19:15.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.520][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[2025-03-07 13:19:15.521][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-07 13:19:15.522][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-07 13:19:15.523][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-07 13:19:15.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.527][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-07 13:19:15.528][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-07 13:19:15.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.531][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-07 13:19:15.531][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-07 13:19:15.532][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-07 13:19:15.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.535][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-07 13:19:15.536][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-07 13:19:15.537][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-07 13:19:15.538][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-07 13:19:15.539][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-07 13:19:15.539][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-07 13:19:15.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.542][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-07 13:19:15.543][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-07 13:19:15.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.546][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-07 13:19:15.547][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-07 13:19:15.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.549][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[2025-03-07 13:19:15.550][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-07 13:19:15.551][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-07 13:19:15.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.554][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-07 13:19:15.555][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-07 13:19:15.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.558][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-07 13:19:15.559][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-07 13:19:15.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.563][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-07 13:19:15.564][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-07 13:19:15.582][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-07 13:19:15.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.585][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-07 13:19:15.586][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-07 13:19:15.587][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-07 13:19:15.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.590][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-07 13:19:15.592][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:15.593][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-07 13:19:15.594][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:15.595][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 13:19:15.596][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:15.597][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 13:19:15.598][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:15.599][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 13:19:15.600][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-07 13:19:15.601][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 13:19:15.602][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:15.603][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-07 13:19:15.604][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 13:19:15.604][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:15.605][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:15.606][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 13:19:15.606][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 13:19:15.606][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 13:19:15.606][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-07 13:19:15.606][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-07 13:19:15.607][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 13:19:15.608][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:15.608][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:15.609][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 13:19:15.610][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:15.611][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:15.611][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 13:19:15.612][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:15.613][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 13:19:15.614][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 13:19:15.614][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:15.615][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:15.616][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-07 13:19:15.618][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:15.619][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-07 13:19:15.620][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:15.620][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 13:19:15.621][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:15.622][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 13:19:15.623][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:15.624][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 13:19:15.624][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-07 13:19:15.625][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 13:19:15.626][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:15.627][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-07 13:19:15.628][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 13:19:15.628][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:15.629][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:15.630][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 13:19:15.630][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 13:19:15.630][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 13:19:15.630][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-07 13:19:15.630][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-07 13:19:15.631][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 13:19:15.632][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:15.632][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:15.633][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 13:19:15.634][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:15.635][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:15.635][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 13:19:15.636][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:15.637][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 13:19:15.638][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 13:19:15.638][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:15.639][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:15.640][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-07 13:19:15.642][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:15.643][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-07 13:19:15.644][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:15.644][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 13:19:15.645][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:15.646][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 13:19:15.647][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:15.648][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 13:19:15.648][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-07 13:19:15.649][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 13:19:15.650][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:15.651][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-07 13:19:15.652][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 13:19:15.652][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:15.653][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:15.654][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:15.655][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 13:19:15.656][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:15.656][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:15.657][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 13:19:15.658][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:15.659][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:15.659][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 13:19:15.660][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:15.661][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 13:19:15.662][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 13:19:15.663][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:15.663][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:15.664][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-07 13:19:15.666][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:15.667][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-07 13:19:15.668][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:15.669][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 13:19:15.669][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:15.670][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 13:19:15.671][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:15.672][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-07 13:19:15.673][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-07 13:19:15.673][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 13:19:15.674][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:15.675][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-07 13:19:15.676][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 13:19:15.677][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:15.677][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:15.678][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:15.679][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-07 13:19:15.680][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:15.681][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:15.681][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 13:19:15.682][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:15.683][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:15.684][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 13:19:15.685][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:15.686][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 13:19:15.686][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 13:19:15.687][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:15.688][self$setPropertyValue]
biodb.DEBUG[2025-03-07 13:19:15.689][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 13:19:15.690][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.698][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[2025-03-07 13:19:15.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.712][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[2025-03-07 13:19:15.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.730][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[2025-03-07 13:19:15.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.751][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[2025-03-07 13:19:15.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.759][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[2025-03-07 13:19:15.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.766][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-07 13:19:15.768][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-07 13:19:15.769][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-07 13:19:15.770][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-07 13:19:15.771][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-07 13:19:15.772][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-07 13:19:15.774][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-07 13:19:15.775][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-07 13:19:15.776][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-07 13:19:15.777][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-07 13:19:15.778][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-07 13:19:15.779][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-07 13:19:15.780][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-07 13:19:15.782][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-07 13:19:15.783][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-07 13:19:15.784][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-07 13:19:15.785][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-07 13:19:15.786][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-07 13:19:15.787][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-07 13:19:15.789][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-07 13:19:15.790][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-07 13:19:15.791][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-07 13:19:15.792][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-07 13:19:15.793][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-07 13:19:15.795][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-07 13:19:15.796][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-07 13:19:15.797][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-07 13:19:15.798][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-07 13:19:15.799][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-07 13:19:15.801][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-07 13:19:15.802][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-07 13:19:15.803][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-07 13:19:15.804][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-07 13:19:15.806][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-07 13:19:15.807][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-07 13:19:15.808][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-07 13:19:15.810][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-07 13:19:15.811][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-07 13:19:15.812][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-07 13:19:15.813][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-07 13:19:15.814][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-07 13:19:15.816][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-07 13:19:15.817][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-07 13:19:15.818][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-07 13:19:15.819][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-07 13:19:15.820][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-07 13:19:15.822][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-07 13:19:15.823][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-07 13:19:15.824][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-07 13:19:15.825][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-07 13:19:15.826][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-07 13:19:15.827][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-07 13:19:15.829][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-07 13:19:15.830][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-07 13:19:15.831][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-07 13:19:15.832][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-07 13:19:15.833][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-07 13:19:15.834][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-07 13:19:15.835][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-07 13:19:15.837][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-07 13:19:15.838][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-07 13:19:15.839][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-07 13:19:15.840][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-07 13:19:15.841][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-07 13:19:15.843][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-07 13:19:15.844][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-07 13:19:15.845][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-07 13:19:15.846][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-07 13:19:15.847][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-07 13:19:15.849][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-07 13:19:15.850][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-07 13:19:15.851][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-07 13:19:15.852][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-07 13:19:15.853][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-07 13:19:15.854][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-07 13:19:15.855][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-07 13:19:15.857][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-07 13:19:15.858][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-07 13:19:15.859][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-07 13:19:15.860][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-07 13:19:15.861][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-07 13:19:15.863][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-07 13:19:15.864][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-07 13:19:15.865][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-07 13:19:15.867][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-07 13:19:15.868][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-07 13:19:15.869][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.871][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:15.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:15.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:15.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:15.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:15.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:15.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.886][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[2025-03-07 13:19:15.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:15.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:15.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.891][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.DEBUG[2025-03-07 13:19:15.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:15.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:15.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:15.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:15.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:15.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:15.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.906][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[2025-03-07 13:19:15.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:15.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:15.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:15.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:15.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:15.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:15.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.921][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[2025-03-07 13:19:15.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:15.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:15.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:15.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:15.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.931][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[2025-03-07 13:19:15.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:15.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:15.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.936][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[2025-03-07 13:19:15.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:15.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:15.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.941][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[2025-03-07 13:19:15.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:15.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:15.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.946][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[2025-03-07 13:19:15.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:15.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:15.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-07 13:19:15.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:15.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:15.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:15.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:15.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:15.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-07 13:19:15.958][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-07 13:19:15.960][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-07 13:19:15.962][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:15.963][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-07 13:19:15.964][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:15.965][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-07 13:19:15.966][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:15.967][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-07 13:19:15.967][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:15.968][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-07 13:19:15.969][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-07 13:19:15.970][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-07 13:19:15.971][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:15.971][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-07 13:19:15.972][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-07 13:19:15.973][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-07 13:19:15.973][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-07 13:19:15.973][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-07 13:19:15.973][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-07 13:19:15.973][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-07 13:19:15.973][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-07 13:19:15.973][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-07 13:19:15.973][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-07 13:19:15.973][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-07 13:19:15.973][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-07 13:19:15.973][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-07 13:19:15.975][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-07 13:19:15.975][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-07 13:19:15.975][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-07 13:19:15.975][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-07 13:19:15.976][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-07 13:19:15.977][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:15.978][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:15.979][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-07 13:19:15.980][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-07 13:19:15.981][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-07 13:19:15.982][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-07 13:19:15.982][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:19:15.982][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-07 13:19:15.983][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-07 13:19:15.984][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-07 13:19:15.985][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-07 13:19:15.986][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-07 13:19:15.986][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-07 13:19:15.987][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-07 13:19:15.989][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-07 13:19:15.990][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-07 13:19:15.991][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-07 13:19:15.993][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-07 13:19:15.994][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-07 13:19:15.997][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-07 13:19:15.998][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-07 13:19:16.000][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-07 13:19:16.009][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-07 13:19:16.010][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-07 13:19:16.011][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-07 13:19:16.012][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-07 13:19:16.013][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-07 13:19:16.014][biodb::testThat]
biodb.INFO [2025-03-07 13:19:16.015][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-03-07 13:19:16.016][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-07 13:19:16.017][biodb::testThat]
biodb.DEBUG[2025-03-07 13:19:16.020][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-07 13:19:16.023][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 13:19:16.025][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-07 13:19:16.026][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 13:19:16.028][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-07 13:19:16.031][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[2025-03-07 13:19:16.035][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-07 13:19:16.036][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-03-07 13:19:16.037][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-07 13:19:16.038][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-03-07 13:19:16.043][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-03-07 13:19:16.044][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-07 13:19:16.045][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-03-07 13:19:16.047][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-07 13:19:16.047][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-07 13:19:16.048][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-07 13:19:16.049][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-07 13:19:16.050][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-07 13:19:16.051][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-07 13:19:16.053][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:16.054][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:16.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:16.060][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:16.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:16.062][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:16.063][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[2025-03-07 13:19:16.064][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-03-07 13:19:16.067][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-07 13:19:16.068][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-07 13:19:16.069][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-03-07 13:19:16.905][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-03-07 13:19:17.082][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-07 13:19:17.084][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-03-07 13:19:17.089][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-03-07 13:19:17.092][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-03-07 13:19:17.094][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-07 13:19:17.095][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-07 13:19:17.096][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-07 13:19:17.098][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-07 13:19:17.099][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:17.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:17.105][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:17.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:17.107][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:17.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-07 13:19:17.113][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:17.114][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:17.115][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.116][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:17.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:17.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.134][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:17.135][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:17.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.136][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.138][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-07 13:19:17.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-07 13:19:17.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.141][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:17.142][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:17.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.144][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.145][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-07 13:19:17.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-07 13:19:17.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.148][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-07 13:19:17.149][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-07 13:19:17.150][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.151][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.152][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-07 13:19:17.153][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-07 13:19:17.154][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.155][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.156][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:17.157][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:17.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.159][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.161][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:17.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-07 13:19:17.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.164][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:17.165][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:17.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.167][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.168][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-07 13:19:17.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-07 13:19:17.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.171][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:17.172][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:17.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.175][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:17.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-07 13:19:17.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.180][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:17.180][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:17.181][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.182][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.184][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-07 13:19:17.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-07 13:19:17.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.188][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:17.188][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:17.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.190][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.191][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-07 13:19:17.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-07 13:19:17.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.196][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:17.197][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:17.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.198][ef$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.200][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-07 13:19:17.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-07 13:19:17.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.204][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:17.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:17.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:17.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:17.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:17.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:17.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-07 13:19:17.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-07 13:19:17.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:17.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:17.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:17.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:17.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:17.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:17.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:17.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:17.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:17.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:17.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-07 13:19:17.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-07 13:19:17.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-07 13:19:17.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-07 13:19:17.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-07 13:19:17.241][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-03-07 13:19:17.246][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-07 13:19:17.247][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-07 13:19:17.248][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-07 13:19:17.249][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-07 13:19:17.250][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-07 13:19:17.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-07 13:19:17.251][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-07 13:19:17.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-07 13:19:17.253][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-07 13:19:17.254][FUN] Functions in observer 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 383 ]
> 
> proc.time()
   user  system elapsed 
 17.127   1.108  27.710

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn2.6801.1165.170
ChebiEntry0.4700.0190.495