Multiple platform build/check report for BioC 3.20 - CHECK results for biodbHmdb on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4756
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4514
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4441
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4406
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*

CHECK results for biodbHmdb on kjohnson1

To the developers/maintainers of the biodbHmdb package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbHmdb.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: biodbHmdb

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbHmdb_1.12.0.tar.gz

StartedAt: 2025-03-18 12:58:39 -0400 (Tue, 18 Mar 2025)

EndedAt: 2025-03-18 12:59:37 -0400 (Tue, 18 Mar 2025)

EllapsedTime: 57.5 seconds

RetCode: 0

Status: WARNINGS

CheckDir: biodbHmdb.Rcheck

Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbHmdb_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/biodbHmdb.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 ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ 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 ‘biodbHmdb’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/biodbHmdb.Rcheck/00check.log’
for details.

Installation output

biodbHmdb.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘biodbHmdb’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c EntryMaker.cpp -o EntryMaker.o
EntryMaker.cpp:6:5: warning: field 'accession_tag' will be initialized after field 'closed' [-Wreorder-ctor]
    accession_tag("<accession>", "</accession>"),
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    closed(true)
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FileEntryMaker.cpp -o FileEntryMaker.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c TagDetector.cpp -o TagDetector.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c XmlSplitter.cpp -o XmlSplitter.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractXmlEntries.cpp -o extractXmlEntries.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-TagDetector.cpp -o test-100-TagDetector.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o biodbHmdb.so EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-biodbHmdb/00new/biodbHmdb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘biodbHmdb’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)

Tests output

biodbHmdb.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(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-03-18 12:59:16.903][biodb::testContext]
biodb.INFO [2025-03-18 12:59:16.908][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-18 12:59:16.909][biodb::testContext] Test context - Tests of independent functions
biodb.INFO [2025-03-18 12:59:16.910][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-18 12:59:16.911][biodb::testContext]
biodb.INFO [2025-03-18 12:59:16.913][biodb::testThat]
biodb.INFO [2025-03-18 12:59:16.915][biodb::testThat] Running test function  test_extractXmlEntries  (" extractXmlEntries() works fine. ").
biodb.INFO [2025-03-18 12:59:16.916][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:16.917][biodb::testThat]
biodb.INFO [2025-03-18 12:59:17.058][biodb::testContext]
biodb.INFO [2025-03-18 12:59:17.060][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-18 12:59:17.062][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-03-18 12:59:17.064][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-18 12:59:17.064][biodb::testContext]
biodb.INFO [2025-03-18 12:59:17.076][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-18 12:59:17.078][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-18 12:59:17.088][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-18 12:59:17.089][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-18 12:59:17.090][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-18 12:59:17.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.094][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-18 12:59:17.124][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-18 12:59:17.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.130][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-18 12:59:17.131][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-18 12:59:17.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.135][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-18 12:59:17.136][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-18 12:59:17.138][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-18 12:59:17.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.142][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-18 12:59:17.143][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-18 12:59:17.144][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-18 12:59:17.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.149][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-18 12:59:17.150][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-18 12:59:17.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.153][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-18 12:59:17.154][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-18 12:59:17.155][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-18 12:59:17.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.160][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-18 12:59:17.162][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-18 12:59:17.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.165][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-18 12:59:17.166][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-18 12:59:17.167][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-18 12:59:17.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.170][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-18 12:59:17.171][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-18 12:59:17.172][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-18 12:59:17.173][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-18 12:59:17.173][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-18 12:59:17.174][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-18 12:59:17.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.176][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.DEBUG[2025-03-18 12:59:17.177][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-18 12:59:17.178][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-18 12:59:17.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.181][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-18 12:59:17.182][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-18 12:59:17.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.185][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-18 12:59:17.186][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-18 12:59:17.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.189][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-18 12:59:17.190][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-18 12:59:17.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.192][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[2025-03-18 12:59:17.193][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-18 12:59:17.194][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-18 12:59:17.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.196][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-18 12:59:17.197][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-18 12:59:17.224][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-18 12:59:17.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.227][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.DEBUG[2025-03-18 12:59:17.228][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-18 12:59:17.229][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-18 12:59:17.230][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-18 12:59:17.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.238][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-18 12:59:17.278][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:17.294][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-18 12:59:17.295][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:17.296][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:17.297][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:17.298][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:17.299][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:17.300][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:17.301][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-18 12:59:17.301][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:17.302][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:17.303][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-18 12:59:17.305][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:17.306][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:17.307][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:17.308][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-18 12:59:17.308][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-18 12:59:17.308][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-18 12:59:17.308][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-18 12:59:17.308][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-18 12:59:17.309][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:17.310][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:17.311][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:17.312][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:17.313][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:17.313][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:17.321][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:17.322][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:17.323][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:17.324][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:17.326][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:17.328][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:17.329][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-18 12:59:17.331][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:17.332][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-18 12:59:17.333][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:17.335][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:17.336][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:17.337][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:17.338][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:17.339][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:17.340][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-18 12:59:17.341][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:17.342][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:17.342][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-18 12:59:17.343][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:17.344][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:17.346][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:17.347][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-18 12:59:17.347][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-18 12:59:17.347][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-18 12:59:17.347][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-18 12:59:17.347][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-18 12:59:17.349][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:17.349][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:17.350][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:17.351][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:17.352][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:17.353][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:17.354][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:17.356][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:17.358][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:17.359][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:17.360][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:17.362][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:17.365][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-18 12:59:17.367][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:17.369][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-18 12:59:17.370][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:17.371][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:17.372][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:17.372][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:17.373][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:17.374][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:17.375][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-18 12:59:17.376][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:17.377][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:17.378][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-18 12:59:17.379][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:17.380][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:17.380][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:17.381][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:17.382][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:17.383][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:17.384][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:17.385][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:17.385][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:17.386][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:17.387][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:17.388][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:17.389][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:17.389][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:17.390][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:17.391][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:17.392][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-18 12:59:17.394][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:17.395][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-18 12:59:17.396][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:17.396][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:17.397][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:17.398][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:17.399][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:17.400][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:17.400][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-18 12:59:17.401][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:17.402][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:17.403][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-18 12:59:17.404][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:17.404][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:17.405][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:17.406][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:17.407][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:17.408][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:17.408][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:17.409][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:17.410][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:17.411][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:17.411][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:17.412][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:17.413][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:17.414][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:17.414][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:17.415][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:17.420][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-18 12:59:17.421][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.425][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[2025-03-18 12:59:17.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.429][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[2025-03-18 12:59:17.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.444][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[2025-03-18 12:59:17.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.449][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[2025-03-18 12:59:17.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.453][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[2025-03-18 12:59:17.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.459][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[2025-03-18 12:59:17.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.464][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[2025-03-18 12:59:17.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.472][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[2025-03-18 12:59:17.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.498][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-18 12:59:17.503][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-18 12:59:17.505][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-18 12:59:17.506][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-18 12:59:17.507][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-18 12:59:17.508][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-18 12:59:17.510][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-18 12:59:17.511][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-18 12:59:17.512][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-18 12:59:17.513][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-18 12:59:17.514][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-18 12:59:17.516][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-18 12:59:17.517][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-18 12:59:17.519][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-18 12:59:17.520][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-18 12:59:17.522][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-18 12:59:17.523][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-18 12:59:17.525][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-18 12:59:17.526][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-18 12:59:17.527][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-18 12:59:17.529][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-18 12:59:17.530][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-18 12:59:17.531][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-18 12:59:17.533][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-18 12:59:17.534][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-18 12:59:17.535][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-18 12:59:17.536][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-18 12:59:17.537][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-18 12:59:17.538][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-18 12:59:17.540][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-18 12:59:17.541][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-18 12:59:17.542][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-18 12:59:17.543][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-18 12:59:17.544][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-18 12:59:17.545][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-18 12:59:17.547][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-18 12:59:17.548][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-18 12:59:17.550][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-18 12:59:17.552][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-18 12:59:17.554][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-18 12:59:17.556][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-18 12:59:17.558][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-18 12:59:17.560][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-18 12:59:17.561][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-18 12:59:17.563][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-18 12:59:17.565][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-18 12:59:17.566][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-18 12:59:17.568][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-18 12:59:17.569][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-18 12:59:17.570][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-18 12:59:17.571][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-18 12:59:17.572][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-18 12:59:17.574][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-18 12:59:17.575][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-18 12:59:17.576][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-18 12:59:17.577][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-18 12:59:17.578][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-18 12:59:17.580][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-18 12:59:17.581][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-18 12:59:17.582][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-18 12:59:17.583][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-18 12:59:17.584][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-18 12:59:17.585][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-18 12:59:17.586][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-18 12:59:17.588][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-18 12:59:17.589][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-18 12:59:17.590][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-18 12:59:17.591][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-18 12:59:17.592][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-18 12:59:17.593][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-18 12:59:17.594][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-18 12:59:17.596][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-18 12:59:17.597][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-18 12:59:17.598][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-18 12:59:17.599][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-18 12:59:17.600][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-18 12:59:17.601][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-18 12:59:17.603][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-18 12:59:17.604][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-18 12:59:17.605][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-18 12:59:17.606][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-18 12:59:17.607][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-18 12:59:17.608][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-18 12:59:17.614][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-18 12:59:17.616][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-18 12:59:17.620][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-18 12:59:17.621][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.623][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:17.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:17.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:17.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:17.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:17.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:17.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:17.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:17.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:17.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:17.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:17.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:17.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:17.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:17.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:17.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:17.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.722][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[2025-03-18 12:59:17.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:17.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:17.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:17.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:17.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:17.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:17.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.740][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[2025-03-18 12:59:17.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:17.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:17.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.745][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[2025-03-18 12:59:17.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:17.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:17.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.751][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[2025-03-18 12:59:17.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:17.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:17.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:17.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:17.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:17.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:17.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:17.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:17.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:17.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:17.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.777][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[2025-03-18 12:59:17.779][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-03-18 12:59:17.791][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-03-18 12:59:17.793][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:17.794][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-18 12:59:17.795][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:17.796][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:17.796][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:17.797][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-03-18 12:59:17.798][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:17.799][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:17.800][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-18 12:59:17.801][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:17.802][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:17.804][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-03-18 12:59:17.805][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:17.807][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-03-18 12:59:17.807][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-03-18 12:59:17.807][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-03-18 12:59:17.807][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-03-18 12:59:17.807][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-03-18 12:59:17.807][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-03-18 12:59:17.807][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-03-18 12:59:17.807][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-03-18 12:59:17.807][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-03-18 12:59:17.807][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-03-18 12:59:17.807][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-03-18 12:59:17.807][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-03-18 12:59:17.807][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-03-18 12:59:17.807][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-03-18 12:59:17.807][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-03-18 12:59:17.807][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-03-18 12:59:17.807][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-03-18 12:59:17.807][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-03-18 12:59:17.808][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:17.809][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-18 12:59:17.809][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-03-18 12:59:17.809][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-03-18 12:59:17.810][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-18 12:59:17.810][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:17.811][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:17.812][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:17.813][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:17.814][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:17.814][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:17.815][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-03-18 12:59:17.815][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-03-18 12:59:17.816][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:17.817][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:17.818][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:17.818][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:17.826][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-03-18 12:59:17.828][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-18 12:59:17.829][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-18 12:59:17.832][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-18 12:59:17.834][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-18 12:59:17.863][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-03-18 12:59:17.864][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-03-18 12:59:17.869][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-03-18 12:59:17.875][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-18 12:59:17.881][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-18 12:59:17.883][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-18 12:59:17.885][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-03-18 12:59:17.886][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2025-03-18 12:59:17.887][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-03-18 12:59:17.887][self$setPropertyValue] Setting property "urls" to "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2025-03-18 12:59:17.888][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:17.889][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:17.890][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2025-03-18 12:59:17.890][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2025-03-18 12:59:17.891][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2025-03-18 12:59:17.918][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-18 12:59:17.919][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-18 12:59:17.920][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-18 12:59:17.922][private$addConnectorRules] Create new rule for URL "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-18 12:59:17.923][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-18 12:59:17.924][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2025-03-18 12:59:17.934][biodb::testThat]
biodb.INFO [2025-03-18 12:59:17.935][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-03-18 12:59:17.937][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:17.938][biodb::testThat]
biodb.TRACE[2025-03-18 12:59:17.944][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-03-18 12:59:17.946][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:17.950][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-18 12:59:17.961][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:17.962][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:17.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:17.969][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:17.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:17.971][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:17.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:17.988][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:17.989][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:17.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:17.991][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:17.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:18.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:18.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.013][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:18.014][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:18.016][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.017][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.048][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:18.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:18.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.054][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:18.056][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:18.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.058][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.059][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:18.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:18.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.062][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:18.063][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:18.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.065][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.066][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:18.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:18.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.069][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:18.070][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:18.071][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.072][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.073][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:18.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:18.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.076][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:18.077][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:18.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.079][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.080][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:18.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:18.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.083][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:18.084][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:18.085][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.086][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.087][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:18.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:18.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.101][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:18.102][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:18.103][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.103][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.105][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:18.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:18.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.108][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:18.109][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:18.110][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.111][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.112][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:18.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:18.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.115][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:18.116][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:18.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.118][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.119][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:18.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:18.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.122][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:18.124][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:18.125][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.126][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.128][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:18.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:18.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.133][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:18.134][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:18.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.136][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.137][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:18.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:18.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.141][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:18.142][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:18.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.143][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.145][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:18.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:18.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.149][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:18.150][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:18.150][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.151][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.152][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:18.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:18.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.156][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:18.157][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:18.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.158][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.160][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:18.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:18.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.163][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:18.164][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:18.165][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.166][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.167][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:18.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:18.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.170][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:18.171][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:18.172][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.172][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.174][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:18.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:18.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.177][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-03-18 12:59:18.178][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:18.179][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.179][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.181][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-03-18 12:59:18.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:18.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:18.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:18.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:18.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:18.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:18.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:18.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.232][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:18.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:18.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.238][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:18.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:18.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.242][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:18.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:18.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.247][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:18.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:18.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.250][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:18.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:18.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.254][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:18.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:18.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.257][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:18.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:18.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.261][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:18.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:18.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:18.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:18.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:18.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:18.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.271][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:18.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:18.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.275][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:18.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:18.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.279][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:18.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:18.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.282][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:18.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:18.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.285][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:18.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:18.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.288][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:18.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:18.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.292][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:18.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:18.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.295][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:18.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:18.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.298][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:18.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:18.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.301][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:18.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:18.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.305][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:18.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:18.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.310][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:18.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:18.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.313][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:18.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:18.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.319][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:18.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:18.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.323][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:18.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:18.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.326][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:18.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:18.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.330][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:18.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:18.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.333][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:18.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:18.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.336][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:18.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:18.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.340][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:18.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:18.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.343][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:18.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:18.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.346][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:18.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:18.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.352][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:18.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:18.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.360][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:18.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:18.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.364][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:18.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:18.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.379][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:18.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:18.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:18.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:18.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:18.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:18.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.392][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:18.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:18.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.395][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:18.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:18.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.398][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:18.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:18.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.408][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:18.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:18.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.411][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:18.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:18.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.416][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:18.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:18.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.419][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:18.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:18.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.423][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:18.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:18.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.426][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:18.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:18.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.430][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:18.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:18.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.435][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:18.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:18.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.441][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:18.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:18.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.445][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:18.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:18.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.448][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-18 12:59:18.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:18.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.452][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:18.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:18.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.455][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:18.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:18.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.458][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:18.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:18.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.464][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-18 12:59:18.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:18.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.487][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:18.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:18.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.503][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:18.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:18.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.506][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:18.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:18.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.510][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:18.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:18.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.513][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:18.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:18.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.516][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:18.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:18.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.520][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:18.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:18.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:18.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:18.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.525][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:18.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:18.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:18.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:18.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:18.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:18.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:18.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:18.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:18.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:18.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:18.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:18.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:18.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:18.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:18.550][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-03-18 12:59:18.553][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-18 12:59:18.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-18 12:59:18.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.555][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-18 12:59:18.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-18 12:59:18.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.558][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-18 12:59:18.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-18 12:59:18.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.563][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-18 12:59:18.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-18 12:59:18.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:18.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:18.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.598][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:18.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:18.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:18.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:18.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:18.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:18.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:18.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:18.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:18.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:18.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:18.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:18.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:18.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:18.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.647][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:18.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:18.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.649][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:18.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:18.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.651][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:18.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:18.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:18.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:18.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:18.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:18.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:18.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:18.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.673][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:18.674][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:18.675][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.676][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:18.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:18.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.689][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:18.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:18.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.701][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:18.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:18.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.705][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:18.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:18.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.709][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:18.710][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:18.711][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.712][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.713][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:18.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:18.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.727][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:18.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:18.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.732][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:18.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:18.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.735][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:18.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:18.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.739][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:18.740][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:18.740][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.741][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.742][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:18.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:18.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.759][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:18.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:18.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.765][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:18.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:18.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.771][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:18.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:18.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.774][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:18.775][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:18.776][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.777][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.778][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:18.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:18.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:18.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:18.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:18.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:18.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:18.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:18.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.803][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:18.804][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:18.804][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.805][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:18.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:18.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.820][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:18.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:18.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.825][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:18.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:18.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.829][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:18.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:18.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.835][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:18.836][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:18.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.838][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.839][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:18.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:18.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.853][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:18.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:18.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.857][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:18.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:18.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.870][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:18.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:18.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.875][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:18.876][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:18.878][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.879][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.880][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:18.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:18.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.894][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:18.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:18.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.898][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:18.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:18.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.901][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:18.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:18.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.905][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:18.906][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:18.906][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.907][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.908][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:18.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:18.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.920][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:18.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:18.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.924][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:18.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:18.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.927][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:18.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:18.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.931][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:18.931][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:18.932][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.933][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.934][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:18.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:18.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.947][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:18.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:18.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.952][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:18.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:18.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.955][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:18.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:18.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.958][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:18.959][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:18.960][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.961][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.963][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:18.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:18.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.978][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:18.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:18.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.984][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:18.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:18.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.991][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:18.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:18.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:18.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:18.996][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:18.997][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:18.998][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.000][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.001][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:19.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:19.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.016][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:19.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:19.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.021][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:19.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:19.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.024][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:19.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:19.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.035][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:19.036][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:19.036][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.037][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.038][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:19.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:19.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.050][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:19.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:19.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.054][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:19.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:19.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.058][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:19.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:19.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.061][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:19.062][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:19.063][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.064][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.064][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:19.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:19.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.077][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:19.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:19.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.081][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:19.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:19.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.085][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:19.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:19.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.088][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:19.090][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:19.090][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.091][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.092][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:19.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:19.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.105][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:19.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:19.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.111][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:19.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:19.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.116][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:19.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:19.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.121][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:19.122][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:19.123][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.123][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.124][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:19.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:19.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.137][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:19.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:19.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.142][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:19.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:19.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.145][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:19.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:19.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.149][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:19.150][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:19.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.151][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.152][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:19.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:19.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.167][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.171][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.174][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.178][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.189][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.190][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.191][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.193][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.208][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:19.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:19.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.213][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:19.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:19.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.217][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:19.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:19.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.222][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:19.223][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:19.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.225][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.225][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:19.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:19.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.238][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:19.239][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:19.240][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.241][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.247][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:19.248][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:19.249][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.249][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.255][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:19.256][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:19.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.258][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.263][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:19.264][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:19.265][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.266][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.271][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:19.272][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:19.273][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.274][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.279][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:19.280][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:19.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.282][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.288][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:19.289][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:19.290][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.291][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.298][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:19.300][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:19.301][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.302][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.308][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:19.309][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:19.310][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.311][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.316][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:19.317][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:19.318][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.319][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.324][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:19.325][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:19.326][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.327][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.332][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.333][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.335][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.340][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:19.341][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:19.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.343][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.349][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:19.351][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:19.351][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.359][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.365][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:19.366][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:19.367][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.368][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.372][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:19.374][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:19.375][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.376][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.381][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:19.382][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:19.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.384][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.390][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:19.391][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:19.392][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.393][ef$get] fields variable is a list.
biodb.INFO [2025-03-18 12:59:19.401][biodb::testThat]
biodb.INFO [2025-03-18 12:59:19.403][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-18 12:59:19.403][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:19.404][biodb::testThat]
biodb.DEBUG[2025-03-18 12:59:19.419][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-03-18 12:59:19.429][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-03-18 12:59:19.434][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:19.436][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-03-18 12:59:19.438][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2025-03-18 12:59:19.439][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:19.441][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2025-03-18 12:59:19.442][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:19.466][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:19.467][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-18 12:59:19.469][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:19.470][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:19.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:19.479][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:19.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:19.482][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:19.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:19.487][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:19.488][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:19.489][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.490][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:19.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:19.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.495][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:19.496][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:19.497][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.498][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.499][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:19.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:19.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.503][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:19.504][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:19.505][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.506][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.507][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:19.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:19.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.518][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:19.520][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:19.521][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.521][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.523][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:19.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:19.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.526][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:19.527][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:19.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.529][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.530][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:19.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:19.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.534][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:19.534][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:19.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.537][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.539][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:19.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:19.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.544][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:19.545][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:19.545][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.546][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.548][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:19.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:19.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.551][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:19.552][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:19.553][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.554][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.555][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:19.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:19.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.559][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:19.560][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:19.561][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.561][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.563][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:19.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:19.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.566][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:19.567][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:19.568][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.569][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.570][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:19.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:19.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.575][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:19.576][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:19.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.578][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.579][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:19.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:19.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.583][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:19.584][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:19.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.586][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.587][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:19.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:19.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.591][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.591][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.592][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.593][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.594][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.598][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:19.599][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:19.600][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.601][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.602][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:19.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:19.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.606][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:19.607][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:19.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.608][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.610][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:19.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:19.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.615][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:19.616][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:19.617][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.618][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.619][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:19.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:19.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.623][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:19.623][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:19.624][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.625][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.626][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:19.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:19.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.630][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-03-18 12:59:19.631][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:19.631][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.632][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.633][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-03-18 12:59:19.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:19.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:19.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:19.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:19.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:19.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:19.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:19.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.648][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:19.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:19.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.658][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:19.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:19.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.661][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:19.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:19.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.665][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:19.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:19.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.668][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:19.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:19.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.671][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:19.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:19.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.675][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:19.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:19.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.682][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:19.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:19.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.686][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:19.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:19.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.690][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:19.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:19.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.694][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:19.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:19.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:19.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:19.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.702][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:19.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:19.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.706][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:19.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:19.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.710][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:19.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:19.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.714][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:19.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:19.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.717][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:19.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:19.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.721][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:19.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:19.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.724][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:19.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:19.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.728][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:19.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:19.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.731][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:19.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:19.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.735][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:19.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:19.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.738][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:19.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:19.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.741][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:19.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:19.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.744][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:19.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:19.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.749][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:19.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:19.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.754][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:19.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:19.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.758][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:19.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:19.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.761][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:19.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:19.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.764][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:19.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:19.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.769][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.777][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.781][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:19.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:19.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.790][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:19.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:19.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.794][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:19.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:19.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.797][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:19.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:19.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.801][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:19.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:19.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:19.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:19.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.807][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:19.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:19.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.811][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:19.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:19.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.814][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:19.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:19.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.817][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:19.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:19.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.820][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:19.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:19.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.823][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:19.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:19.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.827][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:19.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:19.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.830][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:19.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:19.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.833][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:19.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:19.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.836][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:19.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:19.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.839][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:19.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:19.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.844][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:19.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:19.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.849][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-18 12:59:19.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.852][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.856][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.860][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.864][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-18 12:59:19.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:19.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.869][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:19.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:19.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.873][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:19.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:19.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.877][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:19.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:19.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.880][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:19.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:19.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.883][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:19.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:19.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.887][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:19.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:19.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.890][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:19.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:19.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:19.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:19.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.897][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:19.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:19.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:19.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:19.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:19.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:19.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:19.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:19.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:19.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:19.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:19.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:19.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:19.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:19.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:19.930][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2025-03-18 12:59:19.931][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-18 12:59:19.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-18 12:59:19.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.934][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-18 12:59:19.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-18 12:59:19.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.938][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-18 12:59:19.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-18 12:59:19.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-18 12:59:19.952][biodb::testThat]
biodb.INFO [2025-03-18 12:59:19.953][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-18 12:59:19.954][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:19.955][biodb::testThat]
biodb.TRACE[2025-03-18 12:59:19.958][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:19.959][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:19.960][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.961][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:19.962][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2025-03-18 12:59:19.992][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:19.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:19.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:19.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:19.996][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:19.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:19.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:20.000][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:20.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:20.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:20.007][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2025-03-18 12:59:20.009][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-03-18 12:59:20.010][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-03-18 12:59:20.010][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-03-18 12:59:20.012][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:20.013][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:20.015][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-18 12:59:20.016][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:20.017][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-18 12:59:20.018][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-18 12:59:20.019][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-18 12:59:20.021][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-18 12:59:20.022][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-18 12:59:20.024][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-18 12:59:20.024][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-18 12:59:20.027][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:20.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:20.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:20.032][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:20.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:20.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:20.035][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:20.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:20.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:20.039][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:20.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:20.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:20.042][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-18 12:59:20.043][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-18 12:59:20.043][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-03-18 12:59:20.057][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:20.058][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:20.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.068][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:20.070][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2025-03-18 12:59:20.085][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:20.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:20.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:20.089][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:20.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:20.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:20.092][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:20.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:20.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:20.099][function(conn, opt)] With value "1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.".
biodb.DEBUG[2025-03-18 12:59:20.154][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-03-18 12:59:20.156][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2025-03-18 12:59:20.157][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2025-03-18 12:59:20.171][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:20.173][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:20.174][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-18 12:59:20.175][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:20.176][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-18 12:59:20.202][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-18 12:59:20.203][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-18 12:59:20.204][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-18 12:59:20.205][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-18 12:59:20.207][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-18 12:59:20.208][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-18 12:59:20.211][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:20.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:20.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:20.215][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:20.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:20.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:20.219][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:20.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:20.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:20.225][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:20.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:20.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:20.229][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-18 12:59:20.230][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-18 12:59:20.231][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-03-18 12:59:20.245][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:20.246][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:20.247][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.248][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:20.250][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2025-03-18 12:59:20.265][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:20.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:20.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:20.269][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:20.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:20.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:20.274][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:20.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:20.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:20.283][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2025-03-18 12:59:20.286][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2025-03-18 12:59:20.287][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-03-18 12:59:20.288][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-03-18 12:59:20.291][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:20.293][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:20.295][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-18 12:59:20.297][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:20.298][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-18 12:59:20.299][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-18 12:59:20.300][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-18 12:59:20.301][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-18 12:59:20.302][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-18 12:59:20.303][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-18 12:59:20.304][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-18 12:59:20.306][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:20.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:20.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:20.311][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:20.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:20.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:20.315][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:20.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:20.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:20.318][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:20.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:20.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:20.322][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-18 12:59:20.323][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-18 12:59:20.323][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2025-03-18 12:59:20.340][biodb::testThat]
biodb.INFO [2025-03-18 12:59:20.341][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-03-18 12:59:20.342][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:20.343][biodb::testThat]
biodb.TRACE[2025-03-18 12:59:20.359][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:20.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:20.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:20.370][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:20.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:20.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:20.374][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:20.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:20.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:20.389][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-03-18 12:59:20.390][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-03-18 12:59:20.391][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-03-18 12:59:20.393][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:20.394][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:20.396][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-18 12:59:20.397][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:20.398][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-18 12:59:20.399][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-18 12:59:20.401][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-18 12:59:20.402][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-18 12:59:20.404][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-18 12:59:20.405][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-18 12:59:20.406][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-18 12:59:20.408][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:20.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:20.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:20.412][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:20.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:20.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:20.416][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:20.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:20.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:20.421][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:20.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:20.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:20.425][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-18 12:59:20.426][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2025-03-18 12:59:20.444][biodb::testThat]
biodb.INFO [2025-03-18 12:59:20.445][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-03-18 12:59:20.446][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:20.447][biodb::testThat]
biodb.TRACE[2025-03-18 12:59:20.472][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-18 12:59:20.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-18 12:59:20.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:20.476][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-18 12:59:20.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-18 12:59:20.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:20.479][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-18 12:59:20.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-18 12:59:20.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:20.483][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-18 12:59:20.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-18 12:59:20.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:20.538][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-18 12:59:20.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-18 12:59:20.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:20.542][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-18 12:59:20.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-18 12:59:20.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:20.545][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-18 12:59:20.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-18 12:59:20.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:20.549][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-18 12:59:20.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-18 12:59:20.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:20.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-18 12:59:20.561][biodb::testThat]
biodb.INFO [2025-03-18 12:59:20.562][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-18 12:59:20.563][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:20.564][biodb::testThat]
biodb.INFO [2025-03-18 12:59:20.573][biodb::testThat]
biodb.INFO [2025-03-18 12:59:20.574][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-18 12:59:20.575][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:20.575][biodb::testThat]
biodb.INFO [2025-03-18 12:59:20.584][biodb::testThat]
biodb.INFO [2025-03-18 12:59:20.585][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-18 12:59:20.586][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:20.587][biodb::testThat]
biodb.DEBUG[2025-03-18 12:59:20.591][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2025-03-18 12:59:24.595][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2025-03-18 12:59:24.789][biodb::testThat]
biodb.INFO [2025-03-18 12:59:24.790][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-18 12:59:24.791][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:24.792][biodb::testThat]
biodb.DEBUG[2025-03-18 12:59:26.523][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2025-03-18 12:59:26.715][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:26.717][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:26.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.718][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.719][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:26.720][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:26.721][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.722][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.723][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:26.723][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:26.724][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.725][ef$get] fields variable is a list.
biodb.INFO [2025-03-18 12:59:26.727][biodb::testThat]
biodb.INFO [2025-03-18 12:59:26.727][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2025-03-18 12:59:26.728][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:26.729][biodb::testThat]
biodb.DEBUG[2025-03-18 12:59:26.731][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-03-18 12:59:26.790][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-03-18 12:59:26.792][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:26.794][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-03-18 12:59:26.810][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-03-18 12:59:26.812][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:26.813][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:26.814][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:26.815][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:26.816][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:26.817][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-18 12:59:26.819][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:26.820][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:26.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:26.826][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:26.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:26.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:26.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:26.830][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:26.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:26.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.834][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:26.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:26.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:26.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:26.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:26.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:26.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:26.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:26.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:26.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:26.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:26.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:26.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:26.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:26.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:26.900][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-03-18 12:59:26.901][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-03-18 12:59:26.918][biodb::testThat]
biodb.INFO [2025-03-18 12:59:26.919][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-03-18 12:59:26.920][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:26.921][biodb::testThat]
biodb.DEBUG[2025-03-18 12:59:26.930][function(conn, opt)] IDS: [2]: "WRONGB, HMDB0000001"
biodb.DEBUG[2025-03-18 12:59:26.931][private$loadEntries] Creating entries from ids [1]: "WRONGB".
biodb.DEBUG[2025-03-18 12:59:26.932][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-03-18 12:59:26.934][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:26.935][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-03-18 12:59:26.937][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGB".
biodb.TRACE[2025-03-18 12:59:26.938][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-18 12:59:26.939][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-18 12:59:26.940][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:26.941][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:26.942][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:26.943][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-18 12:59:26.945][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:26.946][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:26.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:26.952][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:26.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:26.953][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:26.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:26.956][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:26.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:26.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.959][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:26.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:26.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:26.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:26.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:26.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:26.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:26.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:26.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:26.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:26.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:26.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:26.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:26.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:26.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:26.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:26.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:26.982][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-03-18 12:59:26.983][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-03-18 12:59:26.984][function(conn, opt)] Entries: [2]: "NULL, <environment>"
biodb.INFO [2025-03-18 12:59:27.008][biodb::testThat]
biodb.INFO [2025-03-18 12:59:27.009][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2025-03-18 12:59:27.010][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:27.011][biodb::testThat]
biodb.INFO [2025-03-18 12:59:27.037][biodb::testThat]
biodb.INFO [2025-03-18 12:59:27.038][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2025-03-18 12:59:27.039][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:27.040][biodb::testThat]
biodb.DEBUG[2025-03-18 12:59:27.042][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:27.043][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:27.045][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-18 12:59:27.046][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:27.047][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-18 12:59:27.048][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-18 12:59:27.049][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-18 12:59:27.050][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-18 12:59:27.051][private$doGetEntryIds] COUNT IDS = 2
biodb.INFO [2025-03-18 12:59:27.060][biodb::testThat]
biodb.INFO [2025-03-18 12:59:27.061][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2025-03-18 12:59:27.062][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:27.063][biodb::testThat]
biodb.DEBUG[2025-03-18 12:59:27.066][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:27.067][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:27.069][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-18 12:59:27.070][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:27.071][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-18 12:59:27.072][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-18 12:59:27.073][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-18 12:59:27.074][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-18 12:59:27.075][private$doGetEntryIds] COUNT IDS = 2
biodb.TRACE[2025-03-18 12:59:27.086][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:27.087][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:27.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.089][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.090][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:27.091][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:27.091][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.092][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.093][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:27.094][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:27.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.095][ef$get] fields variable is a list.
biodb.INFO [2025-03-18 12:59:27.096][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-18 12:59:27.097][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-03-18 12:59:27.106][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-03-18 12:59:27.107][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-18 12:59:27.108][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:27.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:27.109][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.111][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.111][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.INFO [2025-03-18 12:59:27.123][biodb::testContext]
biodb.INFO [2025-03-18 12:59:27.125][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-18 12:59:27.126][biodb::testContext] Test context - Test retrieval of entries
biodb.INFO [2025-03-18 12:59:27.127][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-18 12:59:27.128][biodb::testContext]
biodb.INFO [2025-03-18 12:59:27.134][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-18 12:59:27.135][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-18 12:59:27.140][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-18 12:59:27.141][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-18 12:59:27.142][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-18 12:59:27.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.146][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-18 12:59:27.147][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-18 12:59:27.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.149][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.DEBUG[2025-03-18 12:59:27.150][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-18 12:59:27.151][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-18 12:59:27.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.154][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-18 12:59:27.155][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-18 12:59:27.155][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-18 12:59:27.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.159][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-18 12:59:27.159][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-18 12:59:27.160][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-18 12:59:27.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.163][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-18 12:59:27.164][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-18 12:59:27.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.167][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-18 12:59:27.168][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-18 12:59:27.169][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-18 12:59:27.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.172][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-18 12:59:27.173][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-18 12:59:27.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.176][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-18 12:59:27.178][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-18 12:59:27.179][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-18 12:59:27.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.182][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-18 12:59:27.183][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-18 12:59:27.183][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-18 12:59:27.184][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-18 12:59:27.185][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-18 12:59:27.186][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-18 12:59:27.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.188][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[2025-03-18 12:59:27.189][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-18 12:59:27.190][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-18 12:59:27.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.193][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-18 12:59:27.194][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-18 12:59:27.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.196][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[2025-03-18 12:59:27.196][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-18 12:59:27.197][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-18 12:59:27.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.200][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-18 12:59:27.201][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-18 12:59:27.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.203][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[2025-03-18 12:59:27.204][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-18 12:59:27.205][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-18 12:59:27.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.208][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-18 12:59:27.209][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-18 12:59:27.226][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-18 12:59:27.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.230][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-18 12:59:27.231][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-18 12:59:27.231][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-18 12:59:27.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.235][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-18 12:59:27.237][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:27.237][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-18 12:59:27.245][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:27.247][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:27.248][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:27.249][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:27.250][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:27.250][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:27.251][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-18 12:59:27.252][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:27.253][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:27.254][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-18 12:59:27.254][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:27.255][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:27.256][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:27.257][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-18 12:59:27.257][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-18 12:59:27.257][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-18 12:59:27.257][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-18 12:59:27.257][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-18 12:59:27.258][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:27.259][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:27.259][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:27.260][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:27.261][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:27.262][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:27.263][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:27.263][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:27.264][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:27.265][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:27.266][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:27.266][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:27.268][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-18 12:59:27.269][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:27.270][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-18 12:59:27.271][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:27.272][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:27.273][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:27.274][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:27.274][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:27.275][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:27.276][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-18 12:59:27.277][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:27.278][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:27.278][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-18 12:59:27.279][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:27.280][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:27.281][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:27.282][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-18 12:59:27.282][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-18 12:59:27.282][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-18 12:59:27.282][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-18 12:59:27.282][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-18 12:59:27.283][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:27.283][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:27.284][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:27.285][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:27.286][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:27.287][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:27.287][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:27.288][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:27.289][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:27.290][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:27.290][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:27.291][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:27.292][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-18 12:59:27.294][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:27.295][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-18 12:59:27.296][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:27.297][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:27.297][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:27.298][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:27.299][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:27.300][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:27.301][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-18 12:59:27.301][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:27.302][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:27.303][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-18 12:59:27.304][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:27.305][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:27.305][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:27.306][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:27.307][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:27.308][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:27.309][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:27.309][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:27.310][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:27.311][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:27.312][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:27.312][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:27.313][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:27.314][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:27.315][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:27.315][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:27.316][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-18 12:59:27.318][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:27.319][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-18 12:59:27.320][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:27.321][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:27.322][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:27.323][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:27.323][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:27.324][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:27.325][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-18 12:59:27.326][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:27.327][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:27.327][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-18 12:59:27.328][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:27.329][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:27.330][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:27.331][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:27.331][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:27.332][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:27.339][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:27.341][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:27.342][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:27.343][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:27.343][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:27.344][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:27.345][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:27.346][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:27.347][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:27.347][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:27.349][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-18 12:59:27.349][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.354][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[2025-03-18 12:59:27.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.364][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[2025-03-18 12:59:27.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.368][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[2025-03-18 12:59:27.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.371][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[2025-03-18 12:59:27.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.382][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[2025-03-18 12:59:27.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.393][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[2025-03-18 12:59:27.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.404][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[2025-03-18 12:59:27.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.407][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[2025-03-18 12:59:27.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.411][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-18 12:59:27.413][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-18 12:59:27.414][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-18 12:59:27.415][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-18 12:59:27.417][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-18 12:59:27.418][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-18 12:59:27.419][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-18 12:59:27.420][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-18 12:59:27.421][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-18 12:59:27.423][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-18 12:59:27.430][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-18 12:59:27.432][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-18 12:59:27.434][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-18 12:59:27.435][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-18 12:59:27.436][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-18 12:59:27.437][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-18 12:59:27.439][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-18 12:59:27.440][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-18 12:59:27.441][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-18 12:59:27.443][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-18 12:59:27.444][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-18 12:59:27.445][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-18 12:59:27.446][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-18 12:59:27.448][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-18 12:59:27.449][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-18 12:59:27.450][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-18 12:59:27.451][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-18 12:59:27.453][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-18 12:59:27.454][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-18 12:59:27.455][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-18 12:59:27.456][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-18 12:59:27.457][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-18 12:59:27.459][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-18 12:59:27.460][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-18 12:59:27.461][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-18 12:59:27.462][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-18 12:59:27.463][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-18 12:59:27.464][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-18 12:59:27.466][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-18 12:59:27.467][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-18 12:59:27.468][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-18 12:59:27.469][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-18 12:59:27.470][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-18 12:59:27.471][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-18 12:59:27.473][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-18 12:59:27.474][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-18 12:59:27.475][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-18 12:59:27.476][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-18 12:59:27.477][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-18 12:59:27.478][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-18 12:59:27.479][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-18 12:59:27.481][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-18 12:59:27.482][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-18 12:59:27.483][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-18 12:59:27.484][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-18 12:59:27.485][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-18 12:59:27.487][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-18 12:59:27.488][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-18 12:59:27.489][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-18 12:59:27.490][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-18 12:59:27.491][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-18 12:59:27.492][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-18 12:59:27.494][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-18 12:59:27.495][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-18 12:59:27.496][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-18 12:59:27.497][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-18 12:59:27.498][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-18 12:59:27.499][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-18 12:59:27.501][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-18 12:59:27.502][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-18 12:59:27.503][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-18 12:59:27.504][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-18 12:59:27.505][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-18 12:59:27.507][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-18 12:59:27.508][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-18 12:59:27.509][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-18 12:59:27.511][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-18 12:59:27.512][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-18 12:59:27.513][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-18 12:59:27.514][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-18 12:59:27.515][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-18 12:59:27.516][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-18 12:59:27.524][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-18 12:59:27.526][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-18 12:59:27.529][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-18 12:59:27.530][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-18 12:59:27.530][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.532][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:27.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:27.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:27.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:27.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.543][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[2025-03-18 12:59:27.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:27.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:27.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.548][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[2025-03-18 12:59:27.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:27.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:27.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.553][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[2025-03-18 12:59:27.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:27.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:27.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.558][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[2025-03-18 12:59:27.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:27.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:27.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.563][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[2025-03-18 12:59:27.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:27.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:27.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:27.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:27.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:27.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:27.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:27.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:27.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:27.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:27.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.588][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[2025-03-18 12:59:27.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:27.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:27.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.593][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[2025-03-18 12:59:27.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:27.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:27.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:27.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:27.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:27.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:27.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:27.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:27.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:27.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:27.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:27.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:27.628][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-03-18 12:59:27.630][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-03-18 12:59:27.632][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:27.633][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-18 12:59:27.634][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:27.634][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:27.635][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:27.636][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-03-18 12:59:27.637][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:27.638][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:27.639][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-18 12:59:27.639][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:27.640][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:27.641][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-03-18 12:59:27.642][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:27.643][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-03-18 12:59:27.643][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-03-18 12:59:27.643][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-03-18 12:59:27.643][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-03-18 12:59:27.643][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-03-18 12:59:27.643][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-03-18 12:59:27.643][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-03-18 12:59:27.643][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-03-18 12:59:27.643][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-03-18 12:59:27.643][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-03-18 12:59:27.643][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-03-18 12:59:27.643][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-03-18 12:59:27.643][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-03-18 12:59:27.643][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-03-18 12:59:27.643][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-03-18 12:59:27.643][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-03-18 12:59:27.643][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-03-18 12:59:27.643][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-03-18 12:59:27.644][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:27.645][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-18 12:59:27.645][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-03-18 12:59:27.645][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-03-18 12:59:27.646][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-18 12:59:27.646][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:27.647][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:27.648][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:27.649][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:27.649][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:27.650][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:27.651][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-03-18 12:59:27.651][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-03-18 12:59:27.652][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:27.652][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:27.653][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:27.654][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:27.655][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-03-18 12:59:27.656][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-18 12:59:27.658][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-18 12:59:27.659][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-18 12:59:27.661][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-18 12:59:27.664][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-03-18 12:59:27.665][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-03-18 12:59:27.666][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-03-18 12:59:27.667][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-18 12:59:27.668][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-18 12:59:27.669][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-18 12:59:27.670][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-03-18 12:59:27.671][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2025-03-18 12:59:27.672][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-03-18 12:59:27.672][self$setPropertyValue] Setting property "urls" to "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2025-03-18 12:59:27.673][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:27.673][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:27.674][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2025-03-18 12:59:27.675][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2025-03-18 12:59:27.676][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2025-03-18 12:59:27.677][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-18 12:59:27.678][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-18 12:59:27.679][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-18 12:59:27.680][private$addConnectorRules] Create new rule for URL "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-18 12:59:27.681][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-18 12:59:27.682][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2025-03-18 12:59:27.684][biodb::testThat]
biodb.INFO [2025-03-18 12:59:27.684][biodb::testThat] Running test function  test.hmdbmetabolite.nbentries  (" HMDB metabolite returns enough entries. ").
biodb.INFO [2025-03-18 12:59:27.685][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:27.686][biodb::testThat]
biodb.DEBUG[2025-03-18 12:59:27.690][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:27.692][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:27.693][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-18 12:59:27.694][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:27.695][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-18 12:59:27.696][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-18 12:59:27.697][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-18 12:59:27.698][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-18 12:59:27.699][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-18 12:59:27.702][conn$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-03-18 12:59:27.708][biodb::testThat]
biodb.INFO [2025-03-18 12:59:27.709][biodb::testThat] Running test function  test.old.accession  (" We can retrieve entries using old accession numbers. ").
biodb.INFO [2025-03-18 12:59:27.710][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:27.710][biodb::testThat]
biodb.DEBUG[2025-03-18 12:59:27.712][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2025-03-18 12:59:27.719][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-03-18 12:59:27.722][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:27.724][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-03-18 12:59:27.725][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2025-03-18 12:59:27.727][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:27.729][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2025-03-18 12:59:27.731][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:27.732][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:27.733][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-18 12:59:27.735][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:27.736][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:27.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:27.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:27.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:27.745][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:27.746][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[2025-03-18 12:59:27.749][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:27.750][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:27.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.752][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:27.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:27.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.757][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:27.758][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:27.759][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.759][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.761][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:27.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:27.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.764][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:27.765][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:27.766][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.767][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.768][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:27.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:27.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.772][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:27.773][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:27.773][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.774][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.775][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:27.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:27.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.779][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:27.780][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:27.781][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.781][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:27.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:27.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.786][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:27.787][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:27.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.789][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.790][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:27.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:27.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.793][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:27.794][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:27.795][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.796][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.797][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:27.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:27.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.801][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:27.801][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:27.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.803][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.804][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:27.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:27.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.808][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:27.809][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:27.810][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.810][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.812][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:27.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:27.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.815][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:27.816][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:27.817][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.818][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.819][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:27.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:27.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.830][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:27.831][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:27.832][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.833][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.834][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:27.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:27.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.838][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:27.839][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:27.839][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.840][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.841][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:27.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:27.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.845][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:27.846][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:27.846][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.847][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.848][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:27.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:27.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.852][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:27.853][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:27.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.855][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:27.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:27.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.859][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:27.860][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:27.861][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.862][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.863][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:27.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:27.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.866][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:27.867][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:27.868][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.869][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.870][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:27.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:27.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.873][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:27.874][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:27.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.876][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.877][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:27.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:27.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.881][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-03-18 12:59:27.881][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:27.882][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.883][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.884][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-03-18 12:59:27.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:27.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:27.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:27.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:27.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:27.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:27.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:27.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.898][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:27.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:27.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.901][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:27.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:27.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.904][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:27.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:27.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.908][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:27.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:27.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.911][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:27.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:27.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.915][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:27.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:27.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.919][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:27.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:27.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:27.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:27.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.934][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:27.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:27.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.937][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:27.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:27.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.941][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:27.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:27.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.944][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:27.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:27.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.948][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:27.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:27.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.951][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:27.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:27.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.954][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:27.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:27.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.958][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:27.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:27.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.961][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:27.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:27.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.964][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:27.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:27.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.968][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:27.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:27.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.972][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:27.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:27.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.975][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:27.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:27.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.979][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:27.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:27.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.982][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:27.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:27.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.986][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:27.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:27.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.990][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:27.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:27.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.993][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:27.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:27.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:27.996][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:27.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:27.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:27.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.001][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:28.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:28.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.005][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:28.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:28.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.009][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:28.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:28.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.012][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:28.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:28.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.016][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:28.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:28.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.025][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:28.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:28.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.030][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:28.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:28.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.033][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:28.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:28.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.036][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:28.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:28.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:28.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:28.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:28.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:28.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.046][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:28.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:28.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.050][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:28.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:28.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.053][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:28.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:28.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.056][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:28.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:28.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.060][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:28.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:28.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.063][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:28.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:28.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.066][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:28.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:28.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.070][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:28.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:28.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.073][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:28.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:28.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.077][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:28.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:28.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.080][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:28.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:28.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.083][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:28.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:28.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.086][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:28.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:28.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.090][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-18 12:59:28.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:28.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.093][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:28.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:28.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.097][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:28.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:28.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.100][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:28.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:28.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.104][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-18 12:59:28.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:28.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.109][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:28.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:28.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.112][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:28.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:28.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.124][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:28.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:28.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.128][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:28.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:28.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.131][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:28.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:28.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.135][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:28.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:28.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.138][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:28.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:28.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:28.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:28.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.146][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:28.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:28.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:28.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:28.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:28.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:28.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:28.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:28.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:28.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:28.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:28.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:28.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:28.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:28.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:28.172][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2025-03-18 12:59:28.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:28.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:28.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:28.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:28.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:28.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:28.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-18 12:59:28.191][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-18 12:59:28.192][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-03-18 12:59:28.194][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-03-18 12:59:28.194][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-18 12:59:28.195][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:28.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:28.197][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.198][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-18 12:59:28.203][biodb::testContext]
biodb.INFO [2025-03-18 12:59:28.204][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-18 12:59:28.205][biodb::testContext] Test context - Test search of entries
biodb.INFO [2025-03-18 12:59:28.206][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-18 12:59:28.207][biodb::testContext]
biodb.INFO [2025-03-18 12:59:28.213][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-18 12:59:28.215][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-18 12:59:28.220][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-18 12:59:28.221][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-18 12:59:28.222][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-18 12:59:28.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.226][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-18 12:59:28.226][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-18 12:59:28.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.237][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-18 12:59:28.238][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-18 12:59:28.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.242][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-18 12:59:28.243][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-18 12:59:28.243][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-18 12:59:28.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.246][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-18 12:59:28.247][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-18 12:59:28.248][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-18 12:59:28.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.251][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-18 12:59:28.252][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-18 12:59:28.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.255][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-18 12:59:28.256][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-18 12:59:28.257][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-18 12:59:28.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.259][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[2025-03-18 12:59:28.260][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-18 12:59:28.261][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-18 12:59:28.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.264][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-18 12:59:28.265][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-18 12:59:28.266][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-18 12:59:28.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.268][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-18 12:59:28.269][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-18 12:59:28.270][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-18 12:59:28.271][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-18 12:59:28.272][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-18 12:59:28.273][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-18 12:59:28.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.277][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-18 12:59:28.278][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-18 12:59:28.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.282][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-18 12:59:28.283][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-18 12:59:28.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.287][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-18 12:59:28.288][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-18 12:59:28.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.292][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-18 12:59:28.293][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-18 12:59:28.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.297][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-18 12:59:28.298][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-18 12:59:28.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.301][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-18 12:59:28.302][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-18 12:59:28.318][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-18 12:59:28.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.322][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-18 12:59:28.323][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-18 12:59:28.323][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-18 12:59:28.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.327][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-18 12:59:28.329][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:28.330][self$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[2025-03-18 12:59:28.331][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:28.331][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:28.332][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:28.333][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:28.334][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:28.335][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:28.336][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-18 12:59:28.337][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:28.338][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:28.338][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-18 12:59:28.339][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:28.340][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:28.341][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:28.342][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-18 12:59:28.342][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-18 12:59:28.342][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-18 12:59:28.342][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-18 12:59:28.342][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-18 12:59:28.343][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:28.343][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:28.351][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:28.353][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:28.354][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:28.355][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:28.356][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:28.357][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:28.357][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:28.358][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:28.359][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:28.360][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:28.361][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-18 12:59:28.363][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:28.364][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-18 12:59:28.365][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:28.366][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:28.367][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:28.367][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:28.368][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:28.369][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:28.370][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-18 12:59:28.371][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:28.372][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:28.372][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-18 12:59:28.373][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:28.374][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:28.375][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:28.376][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-18 12:59:28.376][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-18 12:59:28.376][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-18 12:59:28.376][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-18 12:59:28.376][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-18 12:59:28.377][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:28.378][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:28.378][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:28.379][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:28.380][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:28.381][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:28.381][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:28.382][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:28.383][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:28.384][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:28.385][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:28.385][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:28.386][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-18 12:59:28.388][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:28.389][self$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[2025-03-18 12:59:28.390][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:28.391][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:28.392][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:28.392][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:28.393][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:28.394][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:28.395][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-18 12:59:28.396][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:28.397][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:28.397][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-18 12:59:28.398][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:28.399][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:28.401][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:28.402][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:28.403][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:28.404][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:28.404][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:28.405][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:28.406][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:28.407][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:28.408][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:28.409][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:28.410][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:28.411][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:28.412][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:28.413][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:28.414][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-18 12:59:28.415][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:28.416][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-18 12:59:28.417][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:28.418][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:28.419][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:28.420][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-18 12:59:28.421][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:28.422][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:28.422][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-18 12:59:28.423][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:28.424][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:28.425][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-18 12:59:28.426][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:28.427][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:28.428][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:28.429][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:28.430][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-18 12:59:28.431][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:28.432][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:28.433][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:28.434][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:28.435][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:28.436][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:28.436][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:28.437][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:28.438][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:28.439][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:28.440][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:28.442][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-18 12:59:28.443][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.450][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[2025-03-18 12:59:28.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.456][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[2025-03-18 12:59:28.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.466][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.DEBUG[2025-03-18 12:59:28.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.470][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[2025-03-18 12:59:28.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.481][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.DEBUG[2025-03-18 12:59:28.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.496][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[2025-03-18 12:59:28.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.512][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[2025-03-18 12:59:28.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.516][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[2025-03-18 12:59:28.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.520][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[2025-03-18 12:59:28.521][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-18 12:59:28.522][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-18 12:59:28.523][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-18 12:59:28.525][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-18 12:59:28.526][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-18 12:59:28.527][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-18 12:59:28.528][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-18 12:59:28.530][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-18 12:59:28.531][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-18 12:59:28.532][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-18 12:59:28.533][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-18 12:59:28.535][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-18 12:59:28.536][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-18 12:59:28.537][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-18 12:59:28.539][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-18 12:59:28.540][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-18 12:59:28.548][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-18 12:59:28.550][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-18 12:59:28.552][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-18 12:59:28.554][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-18 12:59:28.555][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-18 12:59:28.556][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-18 12:59:28.558][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-18 12:59:28.559][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-18 12:59:28.560][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-18 12:59:28.562][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-18 12:59:28.563][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-18 12:59:28.564][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-18 12:59:28.566][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-18 12:59:28.567][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-18 12:59:28.568][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-18 12:59:28.570][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-18 12:59:28.571][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-18 12:59:28.572][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-18 12:59:28.574][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-18 12:59:28.575][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-18 12:59:28.576][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-18 12:59:28.577][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-18 12:59:28.578][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-18 12:59:28.580][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-18 12:59:28.581][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-18 12:59:28.582][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-18 12:59:28.583][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-18 12:59:28.585][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-18 12:59:28.586][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-18 12:59:28.588][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-18 12:59:28.589][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-18 12:59:28.591][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-18 12:59:28.592][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-18 12:59:28.593][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-18 12:59:28.595][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-18 12:59:28.596][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-18 12:59:28.597][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-18 12:59:28.598][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-18 12:59:28.600][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-18 12:59:28.602][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-18 12:59:28.604][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-18 12:59:28.605][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-18 12:59:28.607][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-18 12:59:28.609][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-18 12:59:28.610][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-18 12:59:28.612][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-18 12:59:28.614][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-18 12:59:28.616][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-18 12:59:28.618][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-18 12:59:28.619][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-18 12:59:28.621][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-18 12:59:28.622][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-18 12:59:28.623][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-18 12:59:28.625][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-18 12:59:28.627][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-18 12:59:28.629][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-18 12:59:28.630][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-18 12:59:28.631][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-18 12:59:28.633][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-18 12:59:28.634][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-18 12:59:28.635][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-18 12:59:28.637][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-18 12:59:28.638][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-18 12:59:28.639][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-18 12:59:28.641][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-18 12:59:28.644][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-18 12:59:28.646][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-18 12:59:28.648][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-18 12:59:28.651][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-18 12:59:28.652][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-18 12:59:28.653][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.663][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:28.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:28.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.670][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[2025-03-18 12:59:28.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:28.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:28.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:28.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:28.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:28.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:28.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:28.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:28.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:28.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:28.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.697][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[2025-03-18 12:59:28.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:28.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:28.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.702][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.DEBUG[2025-03-18 12:59:28.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:28.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:28.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:28.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:28.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:28.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:28.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:28.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:28.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.725][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[2025-03-18 12:59:28.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:28.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:28.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.733][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[2025-03-18 12:59:28.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:28.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:28.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:28.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:28.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:28.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:28.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.748][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[2025-03-18 12:59:28.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:28.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:28.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:28.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-18 12:59:28.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:28.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:28.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.766][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[2025-03-18 12:59:28.768][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-03-18 12:59:28.770][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-03-18 12:59:28.772][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:28.773][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-18 12:59:28.774][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:28.774][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-18 12:59:28.775][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:28.776][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-03-18 12:59:28.777][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:28.778][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-18 12:59:28.779][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-18 12:59:28.779][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-18 12:59:28.780][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:28.781][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-03-18 12:59:28.782][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-18 12:59:28.783][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-03-18 12:59:28.783][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-03-18 12:59:28.783][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-03-18 12:59:28.783][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-03-18 12:59:28.783][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-03-18 12:59:28.783][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-03-18 12:59:28.783][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-03-18 12:59:28.783][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-03-18 12:59:28.783][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-03-18 12:59:28.783][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-03-18 12:59:28.783][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-03-18 12:59:28.783][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-03-18 12:59:28.783][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-03-18 12:59:28.783][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-03-18 12:59:28.783][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-03-18 12:59:28.783][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-03-18 12:59:28.783][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-03-18 12:59:28.783][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-03-18 12:59:28.784][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-18 12:59:28.785][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-18 12:59:28.785][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-03-18 12:59:28.785][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-03-18 12:59:28.786][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-18 12:59:28.787][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:28.787][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:28.788][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-18 12:59:28.789][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-18 12:59:28.791][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-18 12:59:28.792][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-18 12:59:28.793][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-03-18 12:59:28.793][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-03-18 12:59:28.794][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:28.795][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:28.796][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-18 12:59:28.797][self$setPropertyValue]
biodb.DEBUG[2025-03-18 12:59:28.799][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-03-18 12:59:28.800][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-18 12:59:28.801][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-18 12:59:28.803][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-18 12:59:28.804][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-18 12:59:28.808][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-03-18 12:59:28.809][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-03-18 12:59:28.810][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-03-18 12:59:28.811][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-18 12:59:28.813][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-18 12:59:28.814][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-18 12:59:28.815][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-03-18 12:59:28.816][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2025-03-18 12:59:28.817][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-03-18 12:59:28.817][self$setPropertyValue] Setting property "urls" to "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2025-03-18 12:59:28.818][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-18 12:59:28.819][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-18 12:59:28.819][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2025-03-18 12:59:28.820][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2025-03-18 12:59:28.821][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2025-03-18 12:59:28.822][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-18 12:59:28.823][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-18 12:59:28.824][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-18 12:59:28.825][private$addConnectorRules] Create new rule for URL "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-18 12:59:28.826][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-18 12:59:28.827][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2025-03-18 12:59:28.829][biodb::testThat]
biodb.INFO [2025-03-18 12:59:28.830][biodb::testThat] Running test function  test.searchMultipleWordsInDescription  (" We can search for multiple words inside description field. ").
biodb.INFO [2025-03-18 12:59:28.830][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-18 12:59:28.832][biodb::testThat]
biodb.DEBUG[2025-03-18 12:59:28.835][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-03-18 12:59:28.836][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2025-03-18 12:59:28.838][private$doSearchForEntries] fields VALUES = and
biodb.INFO [2025-03-18 12:59:28.841][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2025-03-18 12:59:28.843][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2025-03-18 12:59:28.844][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2025-03-18 12:59:28.845][private$doDownload] Downloading HMDB metabolite database at "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" ...
biodb.TRACE[2025-03-18 12:59:28.847][cch$addFilesToCache] Moving files to cache [1]: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.TRACE[2025-03-18 12:59:28.848][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2025-03-18 12:59:28.851][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2025-03-18 12:59:28.853][self$getDownloadPath] Download path of hmdb.metabolites is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2025-03-18 12:59:28.854][self$download] Downloading of hmdb.metabolites completed.
biodb.TRACE[2025-03-18 12:59:28.856][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker13719774b9e4emarker".
biodb.TRACE[2025-03-18 12:59:28.857][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/downloaded.marker".
biodb.DEBUG[2025-03-18 12:59:28.858][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-03-18 12:59:28.860][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-03-18 12:59:28.869][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-03-18 12:59:28.871][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.DEBUG[2025-03-18 12:59:28.873][self$getDownloadPath] Download path of hmdb.metabolites is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2025-03-18 12:59:28.874][private$doExtractDownload] Unzipping /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp...
biodb.DEBUG[2025-03-18 12:59:28.911][private$findXmlDatabaseFile] Found files [1]: "hmdb_two_full_entries.xml" into /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip.
biodb.DEBUG[2025-03-18 12:59:28.913][private$findXmlDatabaseFile] Found XML file /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/hmdb_two_full_entries.xml in ZIP file.
biodb.DEBUG[2025-03-18 12:59:28.914][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2025-03-18 12:59:28.916][private$doExtractDownload] Extract entries from XML file "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/hmdb_two_full_entries.xml", into "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp".
biodb.TRACE[2025-03-18 12:59:28.928][self$addFilesToCache] Moving files to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/HMDB0000001.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/HMDB0000002.xml".
biodb.TRACE[2025-03-18 12:59:28.929][private$doAddFilesToCache] Destination files are [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2025-03-18 12:59:28.931][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-03-18 12:59:28.933][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2025-03-18 12:59:28.936][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker137195865012marker".
biodb.TRACE[2025-03-18 12:59:28.938][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/extracted.marker".
biodb.DEBUG[2025-03-18 12:59:28.939][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-03-18 12:59:28.940][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-18 12:59:28.942][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:28.943][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-18 12:59:28.944][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-18 12:59:28.945][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-18 12:59:28.946][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-18 12:59:28.947][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-18 12:59:28.948][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-18 12:59:28.949][private$doSearchForEntries] Total number of IDs = 2
biodb.DEBUG[2025-03-18 12:59:28.950][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-03-18 12:59:28.951][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-03-18 12:59:28.953][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:28.954][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-03-18 12:59:28.956][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2025-03-18 12:59:28.958][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:28.960][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2025-03-18 12:59:28.961][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:28.962][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:28.963][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-18 12:59:28.965][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:28.965][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:28.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:28.972][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:28.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:28.974][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:28.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:28.979][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:28.981][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:28.982][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.982][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:28.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:28.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.987][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:28.988][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:28.989][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.990][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.991][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:28.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:28.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.995][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:28.996][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:28.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:28.998][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:28.999][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:29.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:29.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.002][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:29.003][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:29.004][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.005][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.006][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:29.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:29.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.012][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:29.013][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:29.014][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.015][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:29.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:29.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.020][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:29.021][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:29.022][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.023][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.024][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:29.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:29.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.037][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:29.038][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:29.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.040][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.041][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:29.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:29.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.045][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:29.046][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:29.047][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.048][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.049][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:29.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:29.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.053][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:29.054][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:29.055][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.056][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.057][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:29.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:29.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.061][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:29.062][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:29.062][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.063][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.065][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:29.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:29.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.069][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:29.070][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:29.070][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.071][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.072][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:29.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:29.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.076][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:29.077][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:29.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.078][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.080][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:29.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:29.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.084][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.085][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.085][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.086][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.087][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.091][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:29.092][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:29.092][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.093][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:29.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:29.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.098][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:29.099][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:29.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.100][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.101][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:29.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:29.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.105][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:29.106][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:29.107][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.107][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.109][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:29.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:29.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.112][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:29.113][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:29.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.114][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.116][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:29.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:29.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.119][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-03-18 12:59:29.120][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:29.121][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.122][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.123][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-03-18 12:59:29.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:29.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:29.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:29.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:29.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:29.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:29.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:29.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.156][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:29.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:29.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.160][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:29.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:29.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.163][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:29.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:29.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.167][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:29.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:29.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.170][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:29.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:29.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.174][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:29.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:29.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.177][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:29.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:29.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.181][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:29.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:29.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.185][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:29.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:29.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.189][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:29.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:29.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.192][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:29.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:29.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:29.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:29.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.198][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:29.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:29.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.202][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:29.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:29.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.205][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:29.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:29.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.209][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:29.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:29.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.214][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:29.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:29.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.217][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:29.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:29.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.220][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:29.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:29.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.224][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:29.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:29.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.227][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:29.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:29.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.231][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:29.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:29.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.234][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:29.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:29.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.246][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:29.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:29.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.251][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:29.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:29.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.255][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:29.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:29.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.258][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:29.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:29.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.262][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:29.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:29.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.265][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:29.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:29.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.269][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:29.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:29.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.272][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.275][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.279][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.282][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:29.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:29.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.285][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:29.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:29.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.288][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:29.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:29.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:29.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:29.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.295][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:29.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:29.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.299][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:29.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:29.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.302][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:29.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:29.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.306][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:29.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:29.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.309][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:29.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:29.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.313][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:29.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:29.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.316][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:29.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:29.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.320][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:29.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:29.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.323][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:29.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:29.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.327][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:29.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:29.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.330][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:29.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:29.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.333][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:29.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:29.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.345][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:29.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:29.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.350][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:29.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:29.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.354][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-18 12:59:29.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.358][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.361][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.365][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.368][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-18 12:59:29.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.373][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:29.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:29.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.376][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:29.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:29.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.380][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:29.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:29.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.383][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:29.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:29.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.386][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:29.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:29.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.390][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:29.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:29.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.393][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:29.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:29.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:29.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:29.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.399][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:29.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:29.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:29.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:29.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:29.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:29.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:29.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:29.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:29.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:29.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:29.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:29.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:29.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:29.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:29.423][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2025-03-18 12:59:29.424][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:29.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:29.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.428][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:29.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:29.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.432][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:29.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:29.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.443][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:29.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:29.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:29.448][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-18 12:59:29.449][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-18 12:59:29.450][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:29.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:29.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:29.457][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:29.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:29.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:29.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:29.461][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2025-03-18 12:59:29.462][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-03-18 12:59:29.464][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:29.465][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-03-18 12:59:29.467][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2025-03-18 12:59:29.468][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-18 12:59:29.470][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2025-03-18 12:59:29.471][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-03-18 12:59:29.472][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-18 12:59:29.473][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-18 12:59:29.475][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:29.476][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:29.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:29.483][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:29.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:29.485][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:29.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:29.490][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:29.491][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:29.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.493][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:29.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:29.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.498][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:29.499][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:29.499][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.500][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.501][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:29.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:29.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.505][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:29.506][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:29.507][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.507][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.509][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:29.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:29.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.512][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:29.513][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:29.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.515][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.516][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:29.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:29.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.519][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:29.520][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:29.521][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.522][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.523][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:29.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:29.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.526][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:29.527][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:29.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.529][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.530][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:29.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:29.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.534][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:29.535][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:29.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.537][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.538][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:29.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:29.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.541][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:29.542][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:29.543][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.544][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.545][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:29.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:29.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.558][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:29.560][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:29.561][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.562][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.563][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:29.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:29.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.566][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:29.567][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:29.568][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.569][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.570][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:29.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:29.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.574][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:29.575][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:29.576][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.576][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.577][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:29.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:29.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.581][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:29.582][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:29.583][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.583][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.585][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:29.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:29.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.589][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.590][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.591][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.591][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.592][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.596][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:29.597][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:29.598][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.598][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:29.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:29.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.603][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:29.604][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:29.605][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.606][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.607][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:29.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:29.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.610][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:29.611][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:29.612][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.613][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.614][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:29.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:29.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.617][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:29.618][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:29.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.620][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.621][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:29.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:29.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.625][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-03-18 12:59:29.626][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:29.627][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.628][ef$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.629][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-03-18 12:59:29.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:29.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:29.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:29.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:29.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:29.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:29.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:29.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.644][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:29.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:29.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.648][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:29.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:29.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.660][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-18 12:59:29.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-18 12:59:29.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.664][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:29.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:29.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.668][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:29.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:29.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.671][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-18 12:59:29.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-18 12:59:29.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.674][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:29.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:29.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:29.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:29.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-18 12:59:29.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-18 12:59:29.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:29.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:29.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:29.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:29.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.691][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:29.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-18 12:59:29.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.696][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:29.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:29.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.700][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:29.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:29.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.705][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:29.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-18 12:59:29.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.709][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:29.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:29.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.712][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:29.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:29.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.715][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:29.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-18 12:59:29.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.718][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:29.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:29.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.721][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:29.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:29.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.725][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:29.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-18 12:59:29.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.728][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:29.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:29.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.731][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:29.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:29.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.734][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:29.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:29.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.738][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:29.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:29.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.741][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:29.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:29.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.744][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-18 12:59:29.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-18 12:59:29.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.754][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:29.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:29.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.760][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:29.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:29.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.764][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-18 12:59:29.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-18 12:59:29.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.767][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.770][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.773][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.777][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:29.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:29.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.780][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:29.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:29.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.783][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:29.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-18 12:59:29.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:29.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:29.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:29.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:29.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.793][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:29.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-18 12:59:29.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.796][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:29.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:29.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.799][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:29.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:29.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.802][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:29.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:29.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.806][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:29.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:29.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.809][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:29.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:29.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.812][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:29.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-18 12:59:29.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.815][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:29.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:29.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.818][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:29.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:29.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.822][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:29.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-18 12:59:29.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.825][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:29.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:29.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.828][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:29.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:29.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.831][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-18 12:59:29.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-18 12:59:29.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.834][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-18 12:59:29.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.838][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.849][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.854][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.857][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-18 12:59:29.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-18 12:59:29.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.861][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:29.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:29.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.865][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:29.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:29.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.868][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:29.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:29.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.871][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:29.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:29.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.875][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-18 12:59:29.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-18 12:59:29.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.878][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:29.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:29.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.881][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:29.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:29.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:29.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:29.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.888][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:29.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-18 12:59:29.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:29.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:29.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:29.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:29.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:29.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:29.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:29.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:29.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:29.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:29.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-18 12:59:29.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-18 12:59:29.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:29.910][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2025-03-18 12:59:29.911][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:29.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:29.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.915][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:29.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:29.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.918][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:29.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:29.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.921][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:29.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:29.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:29.924][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-18 12:59:29.925][private$doSearchForEntries] COUNT IDS = 2
biodb.DEBUG[2025-03-18 12:59:29.927][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:29.927][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:29.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:29.934][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:29.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:29.936][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:29.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:29.952][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-03-18 12:59:29.953][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2025-03-18 12:59:29.954][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2025-03-18 12:59:29.956][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:29.958][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:29.959][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-18 12:59:29.960][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:29.961][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-18 12:59:29.962][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-18 12:59:29.963][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-18 12:59:29.964][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-18 12:59:29.965][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-18 12:59:29.966][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-18 12:59:29.967][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-18 12:59:29.969][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:29.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:29.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.972][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:29.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:29.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.976][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:29.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:29.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.979][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:29.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:29.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.982][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:29.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:29.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.986][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:29.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:29.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:29.989][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:29.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:29.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:29.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:29.993][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-18 12:59:29.994][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-18 12:59:29.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:29.995][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:29.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:30.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:30.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:30.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:30.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-18 12:59:30.005][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:30.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:30.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:30.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:30.009][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:30.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:30.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:30.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:30.013][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:30.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:30.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:30.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:30.016][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:30.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:30.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:30.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:30.020][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:30.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:30.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:30.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:30.023][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:30.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:30.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:30.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:30.027][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:30.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:30.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:30.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:30.030][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2025-03-18 12:59:30.031][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-18 12:59:30.032][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:30.033][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:30.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:30.039][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:30.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:30.041][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:30.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-18 12:59:30.055][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-03-18 12:59:30.057][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2025-03-18 12:59:30.058][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2025-03-18 12:59:30.060][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:30.062][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:30.063][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-18 12:59:30.064][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-18 12:59:30.065][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-18 12:59:30.066][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-18 12:59:30.068][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-18 12:59:30.068][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-18 12:59:30.069][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-18 12:59:30.071][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-18 12:59:30.071][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-18 12:59:30.073][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:30.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:30.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:30.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:30.077][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:30.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:30.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:30.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:30.080][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:30.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:30.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:30.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:30.084][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:30.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:30.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:30.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:30.087][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:30.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:30.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:30.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:30.091][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:30.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:30.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:30.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:30.094][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:30.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:30.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:30.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:30.097][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2025-03-18 12:59:30.098][private$doSearchForEntries] COUNT IDS = 0
biodb.DEBUG[2025-03-18 12:59:30.099][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:30.100][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:30.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:30.106][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:30.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:30.108][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:30.108][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[2025-03-18 12:59:30.110][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:30.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:30.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:30.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:30.113][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:30.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:30.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:30.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:30.117][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:30.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:30.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:30.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:30.120][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:30.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:30.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:30.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:30.123][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:30.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:30.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:30.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:30.127][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:30.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:30.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:30.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-18 12:59:30.130][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-18 12:59:30.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-18 12:59:30.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-18 12:59:30.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-18 12:59:30.133][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-18 12:59:30.134][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-18 12:59:30.135][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-18 12:59:30.136][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:30.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:30.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:30.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:30.144][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:30.145][FUN] Functions in observer BiodbConfig: [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 [2025-03-18 12:59:30.160][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-18 12:59:30.162][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-03-18 12:59:30.163][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-03-18 12:59:30.164][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-18 12:59:30.165][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-18 12:59:30.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-18 12:59:30.167][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-18 12:59:30.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-18 12:59:30.168][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-18 12:59:30.169][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 243 ]
> 
> proc.time()
   user  system elapsed 
  9.101   0.619  15.815

CHECK results for biodbHmdb on kjohnson1

Summary

Command output

Installation output

Tests output

Example timings