Multiple platform build/check report for BioC 3.21 - CHECK results for biodbHmdb on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4783
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4552
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4581
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4533
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4463
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 lconway

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: 1.13.0

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_1.13.0.tar.gz

StartedAt: 2025-03-25 19:44:39 -0400 (Tue, 25 Mar 2025)

EndedAt: 2025-03-25 19:47:19 -0400 (Tue, 25 Mar 2025)

EllapsedTime: 160.0 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_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/biodbHmdb.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.13.0’
* 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 14.0.0 (clang-1400.0.29.202)’
* 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-3.21-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/4.5-x86_64/Resources/library’
* installing *source* package ‘biodbHmdb’ ...
** this is package ‘biodbHmdb’ version ‘1.13.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FileEntryMaker.cpp -o FileEntryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c TagDetector.cpp -o TagDetector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c XmlSplitter.cpp -o XmlSplitter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractXmlEntries.cpp -o extractXmlEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-TagDetector.cpp -o test-100-TagDetector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/4.5-x86_64/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 Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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

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

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-03-25 19:45:25.143][biodb::testContext]
biodb.INFO [2025-03-25 19:45:25.148][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-25 19:45:25.149][biodb::testContext] Test context - Tests of independent functions
biodb.INFO [2025-03-25 19:45:25.151][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-25 19:45:25.152][biodb::testContext]
biodb.INFO [2025-03-25 19:45:25.153][biodb::testThat]
biodb.INFO [2025-03-25 19:45:25.154][biodb::testThat] Running test function  test_extractXmlEntries  (" extractXmlEntries() works fine. ").
biodb.INFO [2025-03-25 19:45:25.155][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-25 19:45:25.156][biodb::testThat]
biodb.INFO [2025-03-25 19:45:25.294][biodb::testContext]
biodb.INFO [2025-03-25 19:45:25.295][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-25 19:45:25.297][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-03-25 19:45:25.298][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-25 19:45:25.299][biodb::testContext]
biodb.INFO [2025-03-25 19:45:25.311][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-25 19:45:25.314][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-25 19:45:25.323][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-25 19:45:25.325][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-25 19:45:25.326][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-25 19:45:25.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.331][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-25 19:45:25.361][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-25 19:45:25.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.366][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-25 19:45:25.368][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-25 19:45:25.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.372][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-25 19:45:25.373][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-25 19:45:25.375][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-25 19:45:25.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.379][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-25 19:45:25.380][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-25 19:45:25.381][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-25 19:45:25.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.385][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-25 19:45:25.386][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-25 19:45:25.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.389][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[2025-03-25 19:45:25.390][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-25 19:45:25.391][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-25 19:45:25.393][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-25 19:45:25.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.397][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-25 19:45:25.398][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-25 19:45:25.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.403][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-25 19:45:25.404][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-25 19:45:25.405][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-25 19:45:25.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.409][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-25 19:45:25.411][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-25 19:45:25.412][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-25 19:45:25.414][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-25 19:45:25.415][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-25 19:45:25.416][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-25 19:45:25.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.421][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-25 19:45:25.422][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-25 19:45:25.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.426][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-25 19:45:25.427][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-25 19:45:25.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.432][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-25 19:45:25.433][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-25 19:45:25.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.438][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-25 19:45:25.439][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-25 19:45:25.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.443][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-25 19:45:25.445][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-25 19:45:25.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.449][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-25 19:45:25.450][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-25 19:45:25.474][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-25 19:45:25.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.480][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-25 19:45:25.481][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-25 19:45:25.483][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-25 19:45:25.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.490][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-25 19:45:25.529][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-25 19:45:25.549][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-25 19:45:25.550][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-25 19:45:25.551][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-25 19:45:25.552][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-25 19:45:25.553][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-25 19:45:25.555][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-25 19:45:25.556][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-25 19:45:25.557][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-25 19:45:25.559][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-25 19:45:25.560][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-25 19:45:25.561][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-25 19:45:25.562][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-25 19:45:25.564][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:45:25.565][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-25 19:45:25.566][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-25 19:45:25.566][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-25 19:45:25.566][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-25 19:45:25.566][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-25 19:45:25.566][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-25 19:45:25.567][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-25 19:45:25.568][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:45:25.569][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:45:25.570][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-25 19:45:25.572][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:45:25.573][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:45:25.574][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-25 19:45:25.575][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:45:25.585][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-25 19:45:25.586][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-25 19:45:25.588][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-25 19:45:25.589][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:45:25.590][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-25 19:45:25.593][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-25 19:45:25.594][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-25 19:45:25.595][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-25 19:45:25.596][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-25 19:45:25.597][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-25 19:45:25.598][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-25 19:45:25.600][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-25 19:45:25.601][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-25 19:45:25.602][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-25 19:45:25.603][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-25 19:45:25.605][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-25 19:45:25.606][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-25 19:45:25.607][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-25 19:45:25.608][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:45:25.610][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-25 19:45:25.611][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-25 19:45:25.611][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-25 19:45:25.611][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-25 19:45:25.611][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-25 19:45:25.611][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-25 19:45:25.612][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-25 19:45:25.614][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:45:25.615][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:45:25.616][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-25 19:45:25.617][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:45:25.619][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:45:25.620][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-25 19:45:25.621][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:45:25.622][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-25 19:45:25.624][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-25 19:45:25.625][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-25 19:45:25.626][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:45:25.627][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-25 19:45:25.630][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-25 19:45:25.631][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-25 19:45:25.632][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-25 19:45:25.634][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-25 19:45:25.635][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-25 19:45:25.637][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-25 19:45:25.638][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-25 19:45:25.639][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-25 19:45:25.641][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-25 19:45:25.642][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-25 19:45:25.643][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-25 19:45:25.645][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-25 19:45:25.646][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-25 19:45:25.647][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:45:25.649][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-25 19:45:25.650][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:45:25.651][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-25 19:45:25.652][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:45:25.654][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:45:25.655][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-25 19:45:25.656][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:45:25.657][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:45:25.659][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-25 19:45:25.660][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:45:25.661][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-25 19:45:25.662][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-25 19:45:25.664][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-25 19:45:25.665][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:45:25.666][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-25 19:45:25.669][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-25 19:45:25.670][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-25 19:45:25.671][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-25 19:45:25.672][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-25 19:45:25.673][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-25 19:45:25.674][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-25 19:45:25.675][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-25 19:45:25.677][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-25 19:45:25.678][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-25 19:45:25.679][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-25 19:45:25.681][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-25 19:45:25.682][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-25 19:45:25.684][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-25 19:45:25.685][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:45:25.687][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-25 19:45:25.689][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:45:25.690][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-25 19:45:25.692][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:45:25.693][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:45:25.694][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-25 19:45:25.695][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:45:25.696][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:45:25.697][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-25 19:45:25.699][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:45:25.700][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-25 19:45:25.701][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-25 19:45:25.702][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-25 19:45:25.703][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:45:25.708][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-25 19:45:25.709][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:25.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:25.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.716][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[2025-03-25 19:45:25.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:25.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:25.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.722][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[2025-03-25 19:45:25.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:25.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:25.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:25.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:25.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.734][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[2025-03-25 19:45:25.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:25.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:25.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:25.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:25.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.743][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[2025-03-25 19:45:25.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:25.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:25.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:25.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:25.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:25.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:25.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:25.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:25.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:25.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:25.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:25.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:25.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.777][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[2025-03-25 19:45:25.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:25.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:25.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:25.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:25.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:25.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:25.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:25.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:25.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:25.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:25.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.804][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-25 19:45:25.816][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-25 19:45:25.818][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-25 19:45:25.820][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-25 19:45:25.822][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-25 19:45:25.824][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-25 19:45:25.825][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-25 19:45:25.827][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-25 19:45:25.829][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-25 19:45:25.830][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-25 19:45:25.832][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-25 19:45:25.834][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-25 19:45:25.835][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-25 19:45:25.837][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-25 19:45:25.838][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-25 19:45:25.839][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-25 19:45:25.841][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-25 19:45:25.842][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-25 19:45:25.844][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-25 19:45:25.846][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-25 19:45:25.847][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-25 19:45:25.849][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-25 19:45:25.851][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-25 19:45:25.852][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-25 19:45:25.854][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-25 19:45:25.856][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-25 19:45:25.857][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-25 19:45:25.859][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-25 19:45:25.861][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-25 19:45:25.862][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-25 19:45:25.864][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-25 19:45:25.865][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-25 19:45:25.867][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-25 19:45:25.868][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-25 19:45:25.870][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-25 19:45:25.871][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-25 19:45:25.873][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-25 19:45:25.875][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-25 19:45:25.877][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-25 19:45:25.878][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-25 19:45:25.880][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-25 19:45:25.882][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-25 19:45:25.883][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-25 19:45:25.885][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-25 19:45:25.887][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-25 19:45:25.889][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-25 19:45:25.890][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-25 19:45:25.892][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-25 19:45:25.894][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-25 19:45:25.896][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-25 19:45:25.898][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-25 19:45:25.899][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-25 19:45:25.901][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-25 19:45:25.902][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-25 19:45:25.903][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-25 19:45:25.905][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-25 19:45:25.906][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-25 19:45:25.908][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-25 19:45:25.910][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-25 19:45:25.912][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-25 19:45:25.913][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-25 19:45:25.915][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-25 19:45:25.916][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-25 19:45:25.918][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-25 19:45:25.919][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-25 19:45:25.921][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-25 19:45:25.923][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-25 19:45:25.924][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-25 19:45:25.926][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-25 19:45:25.928][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-25 19:45:25.930][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-25 19:45:25.932][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-25 19:45:25.934][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-25 19:45:25.936][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-25 19:45:25.938][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-25 19:45:25.940][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-25 19:45:25.942][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-25 19:45:25.943][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-25 19:45:25.946][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-25 19:45:25.947][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-25 19:45:25.949][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-25 19:45:25.951][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-25 19:45:25.953][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-25 19:45:25.961][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-25 19:45:25.964][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-25 19:45:25.968][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-25 19:45:25.969][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:25.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:25.972][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:45:25.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:45:25.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:25.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:25.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:45:25.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:45:25.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:25.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:25.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:25.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:25.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:25.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:45:25.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:45:25.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:26.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:26.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:26.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:26.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:26.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:45:26.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:45:26.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:26.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:26.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:26.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:26.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:26.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:45:26.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:45:26.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:26.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:26.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:26.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:26.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:26.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:45:26.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:45:26.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:26.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:26.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:26.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:26.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:26.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:45:26.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:45:26.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:26.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:26.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:26.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:26.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:26.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:45:26.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:45:26.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:26.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:26.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:26.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:26.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:26.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:45:26.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:45:26.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:26.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:26.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:26.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:26.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:26.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:45:26.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:45:26.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:26.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:26.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:26.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:26.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:26.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:45:26.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:45:26.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:26.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:26.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:26.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:26.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:26.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:45:26.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:45:26.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:26.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:26.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:26.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:26.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:26.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:45:26.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:45:26.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:26.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:26.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:26.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:26.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:26.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:45:26.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:45:26.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:26.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:26.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:26.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:26.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:26.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:45:26.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:45:26.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:26.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:26.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:26.134][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[2025-03-25 19:45:26.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:26.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:45:26.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:45:26.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:26.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:26.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:26.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:45:26.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:45:26.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:45:26.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:45:26.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:26.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:26.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:26.149][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[2025-03-25 19:45:26.152][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-03-25 19:45:26.167][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-03-25 19:45:26.170][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-25 19:45:26.171][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-25 19:45:26.173][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-25 19:45:26.174][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-25 19:45:26.175][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-25 19:45:26.176][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-03-25 19:45:26.178][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-25 19:45:26.179][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-25 19:45:26.180][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-25 19:45:26.181][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-25 19:45:26.182][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-25 19:45:26.184][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-03-25 19:45:26.185][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-25 19:45:26.186][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-03-25 19:45:26.186][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-03-25 19:45:26.186][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-03-25 19:45:26.186][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-03-25 19:45:26.186][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-03-25 19:45:26.186][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-03-25 19:45:26.186][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-03-25 19:45:26.186][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-03-25 19:45:26.186][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-03-25 19:45:26.186][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-03-25 19:45:26.186][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-03-25 19:45:26.186][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-03-25 19:45:26.186][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-03-25 19:45:26.186][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-03-25 19:45:26.186][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-03-25 19:45:26.186][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-03-25 19:45:26.186][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-03-25 19:45:26.186][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-03-25 19:45:26.188][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-25 19:45:26.189][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-25 19:45:26.189][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-03-25 19:45:26.189][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-03-25 19:45:26.191][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-25 19:45:26.192][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:45:26.193][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:45:26.195][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-25 19:45:26.196][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:45:26.197][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:45:26.198][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-25 19:45:26.200][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-03-25 19:45:26.200][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-03-25 19:45:26.201][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-25 19:45:26.202][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-25 19:45:26.203][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-25 19:45:26.204][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:45:26.212][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-03-25 19:45:26.214][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-25 19:45:26.216][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-25 19:45:26.218][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-25 19:45:26.219][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-25 19:45:26.253][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-03-25 19:45:26.255][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-03-25 19:45:26.260][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-03-25 19:45:26.266][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-25 19:45:26.270][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-25 19:45:26.271][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-25 19:45:26.273][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-03-25 19:45:26.274][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2025-03-25 19:45:26.275][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-03-25 19:45:26.275][self$setPropertyValue] Setting property "urls" to "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2025-03-25 19:45:26.276][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-25 19:45:26.277][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-25 19:45:26.278][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2025-03-25 19:45:26.279][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2025-03-25 19:45:26.280][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2025-03-25 19:45:26.311][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-25 19:45:26.313][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-25 19:45:26.314][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-25 19:45:26.316][private$addConnectorRules] Create new rule for URL "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-25 19:45:26.317][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-25 19:45:26.319][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2025-03-25 19:45:26.328][biodb::testThat]
biodb.INFO [2025-03-25 19:45:26.330][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-03-25 19:45:26.331][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-25 19:45:26.332][biodb::testThat]
biodb.TRACE[2025-03-25 19:45:26.337][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-03-25 19:45:26.340][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-25 19:45:26.344][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-25 19:45:26.352][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-25 19:45:26.353][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:45:26.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:45:26.361][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:26.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:26.363][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:26.364][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.TRACE[2025-03-25 19:45:26.377][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:26.379][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:26.380][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.382][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:26.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:26.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.405][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:26.407][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:26.408][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.410][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.449][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:26.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:26.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.456][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:45:26.457][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:45:26.459][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.460][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.462][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:45:26.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:45:26.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.468][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:45:26.469][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:45:26.470][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.471][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.472][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:45:26.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:45:26.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.477][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:45:26.478][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:45:26.479][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.481][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:45:26.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:45:26.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.488][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:26.489][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:26.491][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.492][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:26.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:26.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.500][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:26.501][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:26.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.504][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.506][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:26.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:26.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.523][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:26.524][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:26.526][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.528][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.529][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:26.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:26.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.535][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:26.537][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:26.538][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.539][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.541][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:26.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:26.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.547][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:26.548][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:26.550][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.551][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.553][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:26.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:26.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.558][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:45:26.559][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:45:26.560][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.561][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.563][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:45:26.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:45:26.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.568][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:45:26.570][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:45:26.571][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.572][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.574][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:45:26.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:45:26.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.579][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:45:26.581][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:45:26.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.583][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.584][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:45:26.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:45:26.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.589][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:26.590][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:26.592][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.593][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.595][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:26.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:26.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.599][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:26.600][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:26.601][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.603][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.604][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:26.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:26.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.609][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:45:26.610][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:45:26.611][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.612][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.614][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:45:26.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:45:26.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.618][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:45:26.620][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:45:26.621][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.622][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.623][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:45:26.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:45:26.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.628][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-03-25 19:45:26.629][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:26.630][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.631][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.632][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-03-25 19:45:26.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:26.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:26.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:26.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:26.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:26.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:26.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:26.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.699][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:45:26.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:45:26.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.704][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:45:26.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:45:26.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.709][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:45:26.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:45:26.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.713][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:45:26.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:45:26.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.718][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:45:26.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:45:26.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.722][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:45:26.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:45:26.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.727][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:45:26.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:45:26.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.732][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:45:26.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:45:26.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.737][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:45:26.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:45:26.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.742][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:26.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:26.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.747][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:26.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:26.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.751][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:26.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:26.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.756][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:26.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:26.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.760][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:26.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:26.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.764][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:26.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:26.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.769][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:26.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:26.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.773][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:26.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:26.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.777][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:26.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:26.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.783][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:26.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:26.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.788][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:26.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:26.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.792][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:26.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:26.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.797][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:45:26.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:45:26.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.802][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:45:26.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:45:26.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.806][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:45:26.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:45:26.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.811][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:45:26.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:45:26.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.816][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:45:26.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:45:26.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.821][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:45:26.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:45:26.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.826][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:45:26.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:45:26.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.831][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:45:26.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:45:26.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.837][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:45:26.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:45:26.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.842][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:45:26.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:45:26.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.846][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:45:26.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:45:26.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.850][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:45:26.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:45:26.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.854][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:26.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:26.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.858][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:26.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:26.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.863][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:26.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:26.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.876][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:26.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:26.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.882][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:26.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:26.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:26.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:26.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.891][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:26.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:26.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.896][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:26.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:26.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.900][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:26.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:26.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.904][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:26.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:26.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.909][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:26.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:26.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.913][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:26.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:26.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.918][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:26.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:26.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.923][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:26.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:26.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.928][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:26.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:26.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.932][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:45:26.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:45:26.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.937][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:45:26.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:45:26.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.942][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:45:26.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:45:26.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.946][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-25 19:45:26.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:45:26.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.950][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:45:26.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:45:26.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.955][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:45:26.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:45:26.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.959][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:45:26.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:45:26.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.964][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-25 19:45:26.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:45:26.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.989][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:26.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:26.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:26.996][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:26.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:26.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:26.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.000][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:27.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:27.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.004][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:27.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:27.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.009][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:27.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:27.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.014][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:45:27.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:45:27.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.020][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:45:27.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:45:27.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:27.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:27.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.030][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:45:27.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:45:27.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:27.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:27.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:27.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:27.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:27.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:27.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:27.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:27.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:27.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:27.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:27.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:27.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-25 19:45:27.106][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-03-25 19:45:27.110][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-25 19:45:27.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-25 19:45:27.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.115][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-25 19:45:27.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-25 19:45:27.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.120][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-25 19:45:27.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-25 19:45:27.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.125][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-25 19:45:27.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-25 19:45:27.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:27.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:27.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.162][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:45:27.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:45:27.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:27.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:27.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:27.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:27.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:27.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:27.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:27.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:27.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:27.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:27.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:27.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:27.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.207][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:45:27.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:45:27.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.211][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:45:27.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:45:27.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.217][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:45:27.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:45:27.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:27.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:27.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:27.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:27.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:27.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:27.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.253][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:27.255][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:27.256][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.257][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:27.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:27.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.276][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:27.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:27.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.283][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:27.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:27.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.296][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:27.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:27.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.301][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:27.303][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:27.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.305][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.306][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:27.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:27.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:27.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:27.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:27.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:27.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:27.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:27.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.338][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:27.340][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:27.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.342][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.343][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:27.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:27.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.360][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:27.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:27.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.364][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:27.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:27.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.369][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:27.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:27.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.374][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:27.375][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:27.376][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.377][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.378][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:27.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:27.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.395][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:45:27.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:45:27.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.401][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:45:27.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:45:27.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.407][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:45:27.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:45:27.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.412][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:45:27.414][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:45:27.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.416][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.417][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:45:27.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:45:27.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.433][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:27.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:27.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.439][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:27.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:27.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.443][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:27.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:27.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.448][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:27.449][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:27.450][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.451][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.452][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:27.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:27.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.468][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:27.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:27.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.474][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:27.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:27.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.479][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:27.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:27.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.491][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:27.492][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:27.493][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.494][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.495][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:27.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:27.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.511][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:45:27.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:45:27.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.517][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:45:27.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:45:27.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.521][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:45:27.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:45:27.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.527][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:45:27.528][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:45:27.529][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.530][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.532][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:45:27.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:45:27.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.548][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:45:27.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:45:27.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.554][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:45:27.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:45:27.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.560][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:45:27.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:45:27.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.566][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:45:27.567][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:45:27.569][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.570][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.571][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:45:27.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:45:27.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.589][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:45:27.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:45:27.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.594][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:45:27.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:45:27.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.599][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:45:27.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:45:27.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.604][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:45:27.605][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:45:27.606][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.608][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.609][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:45:27.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:45:27.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.626][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:27.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:27.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.631][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:27.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:27.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.637][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:27.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:27.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.642][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:27.644][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:27.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.646][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.647][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:27.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:27.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.665][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:27.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:27.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.671][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:27.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:27.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.676][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:27.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:27.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.681][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:27.690][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:27.692][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.693][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.695][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:27.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:27.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.712][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:27.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:27.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.719][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:27.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:27.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.725][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:27.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:27.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.731][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:27.733][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:27.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.735][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.737][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:27.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:27.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.759][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:27.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:27.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.765][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:27.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:27.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.771][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:27.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:27.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.777][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:27.779][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:27.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.782][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.783][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:27.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:27.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.800][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:45:27.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:45:27.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.807][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:45:27.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:45:27.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.813][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:45:27.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:45:27.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.819][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:45:27.821][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:45:27.822][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.823][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.825][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:45:27.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:45:27.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.843][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:45:27.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:45:27.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.848][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:45:27.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:45:27.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.855][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:45:27.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:45:27.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.860][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:45:27.861][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:45:27.863][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.864][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.865][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:45:27.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:45:27.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.883][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:45:27.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:45:27.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.888][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:45:27.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:45:27.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.894][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:45:27.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:45:27.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.899][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:45:27.901][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:45:27.902][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.903][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.905][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:45:27.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:45:27.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.930][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:45:27.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:45:27.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.937][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:45:27.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:45:27.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.942][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:45:27.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:45:27.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.948][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:45:27.949][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:45:27.950][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.951][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.952][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:45:27.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:45:27.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.969][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:27.971][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:27.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.974][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.981][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:45:27.983][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:45:27.985][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.986][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:27.995][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:45:27.996][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:45:27.998][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:27.999][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.007][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:45:28.009][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:45:28.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.012][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.020][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:28.022][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:28.023][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.025][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.033][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:28.034][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:28.036][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.037][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.045][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:28.047][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:28.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.050][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.057][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:28.059][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:28.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.062][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.069][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:45:28.071][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:45:28.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.074][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.080][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:45:28.082][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:45:28.083][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.085][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.093][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:45:28.095][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:45:28.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.098][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.105][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:45:28.107][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:45:28.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.110][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.118][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:28.119][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:28.121][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.122][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.130][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:28.132][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:28.134][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.135][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.150][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:28.152][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:28.153][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.155][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.163][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:28.165][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:28.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.168][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.175][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:28.177][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:28.179][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.180][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.187][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:45:28.188][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:45:28.190][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.191][ef$get] fields variable is a list.
biodb.INFO [2025-03-25 19:45:28.204][biodb::testThat]
biodb.INFO [2025-03-25 19:45:28.205][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-25 19:45:28.207][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-25 19:45:28.208][biodb::testThat]
biodb.DEBUG[2025-03-25 19:45:28.227][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-03-25 19:45:28.236][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-03-25 19:45:28.242][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:45:28.244][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-03-25 19:45:28.248][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2025-03-25 19:45:28.250][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-25 19:45:28.252][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2025-03-25 19:45:28.254][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-03-25 19:45:28.289][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-25 19:45:28.291][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-25 19:45:28.294][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-25 19:45:28.295][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:45:28.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:45:28.304][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:45:28.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:45:28.307][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:45:28.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-25 19:45:28.313][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:28.315][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:28.317][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.318][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:28.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:28.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.325][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:28.327][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:28.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.330][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.332][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:28.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:28.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.337][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:45:28.339][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:45:28.340][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.341][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.343][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:45:28.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:45:28.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.348][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:45:28.350][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:45:28.351][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.352][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.361][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:45:28.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:45:28.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.367][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:45:28.369][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:45:28.370][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.371][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:45:28.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:45:28.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.378][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:28.380][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:28.381][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.382][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.384][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:28.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:28.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.389][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:28.391][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:28.392][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.394][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.396][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:28.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:28.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.401][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:28.402][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:28.403][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.404][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.405][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:28.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:28.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.411][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:28.413][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:28.414][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.415][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.417][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:28.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:28.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.422][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:28.423][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:28.424][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.425][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.427][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:28.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:28.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.432][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:45:28.433][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:45:28.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.436][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.437][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:45:28.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:45:28.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.442][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:45:28.444][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:45:28.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.446][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.448][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:45:28.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:45:28.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.453][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:45:28.454][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:45:28.455][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.457][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.458][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:45:28.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:45:28.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.463][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:28.464][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:28.465][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.466][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.468][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:28.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:28.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.473][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:28.474][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:28.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.476][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.477][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:28.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:28.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.483][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:45:28.484][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:45:28.485][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.487][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.488][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:45:28.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:45:28.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.494][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:45:28.495][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:45:28.497][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.498][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.500][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:45:28.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:45:28.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.505][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-03-25 19:45:28.508][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:28.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.511][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.513][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-03-25 19:45:28.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:28.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:28.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:28.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:28.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:28.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:28.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:28.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.535][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:45:28.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:45:28.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.540][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:45:28.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:45:28.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.553][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:45:28.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:45:28.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.558][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:45:28.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:45:28.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.563][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:45:28.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:45:28.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.568][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:45:28.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:45:28.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:45:28.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:45:28.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:45:28.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:45:28.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:45:28.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:45:28.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.589][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:28.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:28.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.595][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:28.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:28.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:28.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:45:28.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.605][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:28.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:28.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.611][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:28.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:28.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.616][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:28.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:45:28.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.621][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:28.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:28.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.627][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:28.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:28.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.633][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:28.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:45:28.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.639][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:28.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:28.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.644][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:28.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:28.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.649][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:28.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:45:28.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.654][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:45:28.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:45:28.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.659][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:45:28.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:45:28.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.663][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:45:28.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:45:28.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.668][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:45:28.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:45:28.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.672][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:45:28.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:45:28.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.677][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:45:28.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:45:28.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.682][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:45:28.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:45:28.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.687][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:45:28.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:45:28.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.692][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:45:28.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:45:28.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.696][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:45:28.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:45:28.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.702][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:45:28.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:45:28.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.707][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:45:28.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:45:28.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.730][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:28.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:28.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.737][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:28.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:28.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.752][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:28.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:45:28.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.758][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:28.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:28.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:28.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:28.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:28.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:45:28.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.821][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:28.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:28.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.827][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:28.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:28.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.833][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:28.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:28.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.838][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:28.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:28.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.844][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:28.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:28.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.850][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:28.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:45:28.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.856][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:28.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:28.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.862][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:28.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:28.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.867][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:28.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:28.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.872][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:45:28.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:45:28.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.878][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:45:28.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:45:28.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.883][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:45:28.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:45:28.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.888][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-25 19:45:28.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:45:28.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.893][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:45:28.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:45:28.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.898][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:45:28.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:45:28.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.903][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:45:28.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:45:28.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.908][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-25 19:45:28.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:45:28.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.915][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:28.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:28.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.920][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:28.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:28.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.925][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:28.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:28.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.930][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:28.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:28.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.935][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:28.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:28.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.941][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:45:28.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:45:28.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.947][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:45:28.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:45:28.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:28.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:28.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.958][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:45:28.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:45:28.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:28.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:28.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:28.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:28.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:28.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:28.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:28.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:28.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:28.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:28.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:28.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:45:28.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:45:28.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:28.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-25 19:45:29.000][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2025-03-25 19:45:29.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-25 19:45:29.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-25 19:45:29.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-25 19:45:29.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-25 19:45:29.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.012][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-25 19:45:29.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-25 19:45:29.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-25 19:45:29.029][biodb::testThat]
biodb.INFO [2025-03-25 19:45:29.031][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-25 19:45:29.032][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-25 19:45:29.034][biodb::testThat]
biodb.TRACE[2025-03-25 19:45:29.038][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:29.040][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:29.041][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.042][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-25 19:45:29.044][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2025-03-25 19:45:29.083][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:29.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:29.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.089][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:29.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:29.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.094][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:29.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:29.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-25 19:45:29.105][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2025-03-25 19:45:29.107][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-03-25 19:45:29.109][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-03-25 19:45:29.110][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-03-25 19:45:29.113][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:45:29.115][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:45:29.116][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-25 19:45:29.118][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:45:29.120][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-25 19:45:29.122][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-25 19:45:29.123][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-25 19:45:29.125][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-25 19:45:29.126][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-25 19:45:29.127][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-25 19:45:29.128][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-25 19:45:29.130][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:29.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:29.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.136][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:29.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:29.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.141][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:29.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:29.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.147][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:29.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:29.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-25 19:45:29.152][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-25 19:45:29.153][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-25 19:45:29.155][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-03-25 19:45:29.173][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:45:29.175][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:45:29.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.178][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-25 19:45:29.180][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2025-03-25 19:45:29.206][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:45:29.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:45:29.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.212][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:45:29.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:45:29.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.217][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:45:29.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:45:29.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-25 19:45:29.226][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[2025-03-25 19:45:29.299][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-03-25 19:45:29.300][private$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[2025-03-25 19:45:29.301][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2025-03-25 19:45:29.318][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:45:29.321][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:45:29.323][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-25 19:45:29.325][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:45:29.326][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-25 19:45:29.353][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-25 19:45:29.355][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-25 19:45:29.356][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-25 19:45:29.358][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-25 19:45:29.359][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-25 19:45:29.361][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-25 19:45:29.363][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:45:29.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:45:29.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.368][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:45:29.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:45:29.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.373][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:45:29.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:45:29.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.378][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:45:29.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:45:29.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-25 19:45:29.384][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-25 19:45:29.385][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-25 19:45:29.386][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-03-25 19:45:29.403][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:29.405][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:29.406][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.408][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-25 19:45:29.410][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2025-03-25 19:45:29.429][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:29.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:29.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.436][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:29.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:29.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.441][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:29.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:29.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-25 19:45:29.449][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2025-03-25 19:45:29.451][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2025-03-25 19:45:29.452][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-03-25 19:45:29.454][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-03-25 19:45:29.455][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:45:29.457][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:45:29.459][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-25 19:45:29.461][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:45:29.462][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-25 19:45:29.464][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-25 19:45:29.466][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-25 19:45:29.467][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-25 19:45:29.468][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-25 19:45:29.469][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-25 19:45:29.470][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-25 19:45:29.472][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:29.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:29.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.477][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:29.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:29.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.482][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:29.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:29.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.487][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:29.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:45:29.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-25 19:45:29.492][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-25 19:45:29.494][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-25 19:45:29.495][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2025-03-25 19:45:29.518][biodb::testThat]
biodb.INFO [2025-03-25 19:45:29.520][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-03-25 19:45:29.521][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-25 19:45:29.522][biodb::testThat]
biodb.TRACE[2025-03-25 19:45:29.539][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:29.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:29.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.544][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:29.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:29.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.556][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:29.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:29.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-25 19:45:29.576][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-03-25 19:45:29.578][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-03-25 19:45:29.579][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-03-25 19:45:29.581][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:45:29.584][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:45:29.586][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-25 19:45:29.588][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:45:29.589][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-25 19:45:29.590][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-25 19:45:29.592][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-25 19:45:29.593][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-25 19:45:29.595][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-25 19:45:29.596][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-25 19:45:29.597][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-25 19:45:29.600][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:29.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:29.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.605][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:29.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:29.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.609][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:29.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:29.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.614][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:45:29.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:45:29.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-25 19:45:29.619][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-25 19:45:29.620][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2025-03-25 19:45:29.643][biodb::testThat]
biodb.INFO [2025-03-25 19:45:29.644][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-03-25 19:45:29.646][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-25 19:45:29.647][biodb::testThat]
biodb.TRACE[2025-03-25 19:45:29.673][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-25 19:45:29.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-25 19:45:29.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.679][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-25 19:45:29.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-25 19:45:29.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.684][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-25 19:45:29.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-25 19:45:29.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.689][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-25 19:45:29.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-25 19:45:29.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.750][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-25 19:45:29.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-25 19:45:29.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.757][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-25 19:45:29.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-25 19:45:29.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.761][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-25 19:45:29.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-25 19:45:29.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:45:29.766][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-25 19:45:29.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-25 19:45:29.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:45:29.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-25 19:45:29.780][biodb::testThat]
biodb.INFO [2025-03-25 19:45:29.782][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-25 19:45:29.783][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-25 19:45:29.784][biodb::testThat]
biodb.INFO [2025-03-25 19:45:29.795][biodb::testThat]
biodb.INFO [2025-03-25 19:45:29.796][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-25 19:45:29.797][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-25 19:45:29.799][biodb::testThat]
biodb.INFO [2025-03-25 19:45:29.809][biodb::testThat]
biodb.INFO [2025-03-25 19:45:29.810][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-25 19:45:29.812][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-25 19:45:29.813][biodb::testThat]
biodb.DEBUG[2025-03-25 19:45:29.817][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2025-03-25 19:45:59.624][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2025-03-25 19:45:59.680][biodb::testThat]
biodb.INFO [2025-03-25 19:45:59.681][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-25 19:45:59.683][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-25 19:45:59.685][biodb::testThat]
biodb.DEBUG[2025-03-25 19:46:20.567][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2025-03-25 19:46:20.611][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:20.612][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:20.614][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:20.615][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:20.617][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:20.618][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:20.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:20.621][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:20.622][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:20.623][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:20.625][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:20.626][ef$get] fields variable is a list.
biodb.INFO [2025-03-25 19:46:20.628][biodb::testThat]
biodb.INFO [2025-03-25 19:46:20.629][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2025-03-25 19:46:20.630][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-25 19:46:20.632][biodb::testThat]
biodb.DEBUG[2025-03-25 19:46:20.634][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-03-25 19:46:20.716][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.INFO [2025-03-25 19:46:20.719][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2025-03-25 19:46:20.721][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2025-03-25 19:46:20.722][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2025-03-25 19:46:20.724][private$doDownload] Downloading HMDB metabolite database at "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" ...
biodb.TRACE[2025-03-25 19:46:20.726][cch$addFilesToCache] Moving files to cache [1]: "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.TRACE[2025-03-25 19:46:20.728][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2025-03-25 19:46:20.731][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2025-03-25 19:46:20.733][self$getDownloadPath] Download path of hmdb.metabolites is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2025-03-25 19:46:20.735][self$download] Downloading of hmdb.metabolites completed.
biodb.TRACE[2025-03-25 19:46:20.738][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker143fd2cd4b97bmarker".
biodb.TRACE[2025-03-25 19:46:20.740][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/downloaded.marker".
biodb.DEBUG[2025-03-25 19:46:20.741][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-03-25 19:46:20.743][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-03-25 19:46:20.745][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-03-25 19:46:20.747][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.DEBUG[2025-03-25 19:46:20.749][self$getDownloadPath] Download path of hmdb.metabolites is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2025-03-25 19:46:20.750][private$doExtractDownload] Unzipping /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp...
biodb.DEBUG[2025-03-25 19:46:20.770][private$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[2025-03-25 19:46:20.771][private$findXmlDatabaseFile] Found XML file /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/hmdb_two_full_entries.xml in ZIP file.
biodb.DEBUG[2025-03-25 19:46:20.773][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2025-03-25 19:46:20.775][private$doExtractDownload] Extract entries from XML file "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/hmdb_two_full_entries.xml", into "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp".
biodb.TRACE[2025-03-25 19:46:20.788][self$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[2025-03-25 19:46:20.790][private$doAddFilesToCache] Destination files are [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2025-03-25 19:46:20.792][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-03-25 19:46:20.793][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2025-03-25 19:46:20.797][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker143fd41dd513bmarker".
biodb.TRACE[2025-03-25 19:46:20.799][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/extracted.marker".
biodb.DEBUG[2025-03-25 19:46:20.801][self$addFilesToCache] Done adding files.
biodb.TRACE[2025-03-25 19:46:20.837][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-03-25 19:46:20.839][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-25 19:46:20.840][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-25 19:46:20.842][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-03-25 19:46:20.844][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:46:20.853][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-25 19:46:20.856][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-25 19:46:20.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-25 19:46:20.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:20.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:20.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:20.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:20.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:20.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-25 19:46:20.959][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:46:20.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:46:20.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:20.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:20.965][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:46:20.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:46:20.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:20.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:20.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:20.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:20.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:20.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:21.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:21.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:21.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:21.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:21.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:21.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:21.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:21.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:21.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:21.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:21.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:21.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:21.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:21.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:21.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:21.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:21.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:21.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:21.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:21.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-25 19:46:21.062][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-03-25 19:46:21.063][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-03-25 19:46:21.110][biodb::testThat]
biodb.INFO [2025-03-25 19:46:21.112][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-03-25 19:46:21.113][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-25 19:46:21.114][biodb::testThat]
biodb.DEBUG[2025-03-25 19:46:21.135][function(conn, opt)] IDS: [2]: "WRONGB, HMDB0000001"
biodb.DEBUG[2025-03-25 19:46:21.145][private$loadEntries] Creating entries from ids [1]: "WRONGB".
biodb.DEBUG[2025-03-25 19:46:21.147][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-03-25 19:46:21.151][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:46:21.153][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-03-25 19:46:21.165][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGB".
biodb.TRACE[2025-03-25 19:46:21.168][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-25 19:46:21.170][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-25 19:46:21.171][conn$getEntryContent] 0 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-03-25 19:46:21.174][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:46:21.189][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-25 19:46:21.191][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-25 19:46:21.193][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-25 19:46:21.195][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:21.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:21.216][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:21.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:21.219][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:21.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-25 19:46:21.225][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:46:21.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:46:21.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:21.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:21.231][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:46:21.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:46:21.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:21.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:21.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:21.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:21.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:21.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:21.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:21.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:21.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:21.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:21.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:21.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:21.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:21.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:21.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:21.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:21.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:21.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:21.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:21.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:21.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:21.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:21.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:21.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:21.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:21.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-25 19:46:21.327][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2025-03-25 19:46:21.329][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-03-25 19:46:21.336][function(conn, opt)] Entries: [2]: "NULL, <environment>"
biodb.INFO [2025-03-25 19:46:21.360][biodb::testThat]
biodb.INFO [2025-03-25 19:46:21.361][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2025-03-25 19:46:21.363][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-25 19:46:21.365][biodb::testThat]
biodb.INFO [2025-03-25 19:46:21.446][biodb::testThat]
biodb.INFO [2025-03-25 19:46:21.448][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2025-03-25 19:46:21.449][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-25 19:46:21.451][biodb::testThat]
biodb.DEBUG[2025-03-25 19:46:21.462][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:46:21.466][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:46:21.468][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-25 19:46:21.471][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:46:21.472][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-25 19:46:21.483][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-25 19:46:21.485][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-25 19:46:21.486][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-25 19:46:21.488][private$doGetEntryIds] COUNT IDS = 2
biodb.INFO [2025-03-25 19:46:21.514][biodb::testThat]
biodb.INFO [2025-03-25 19:46:21.516][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2025-03-25 19:46:21.517][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-25 19:46:21.519][biodb::testThat]
biodb.DEBUG[2025-03-25 19:46:21.529][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:46:21.532][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:46:21.535][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-25 19:46:21.537][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:46:21.538][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-25 19:46:21.547][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-25 19:46:21.549][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-25 19:46:21.551][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-25 19:46:21.552][private$doGetEntryIds] COUNT IDS = 2
biodb.TRACE[2025-03-25 19:46:21.577][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:21.578][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:21.580][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:21.581][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:21.583][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:21.584][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:21.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:21.616][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:21.617][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:21.619][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:21.621][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:21.622][ef$get] fields variable is a list.
biodb.INFO [2025-03-25 19:46:21.631][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-25 19:46:21.633][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-03-25 19:46:21.652][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-03-25 19:46:21.654][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-25 19:46:21.655][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:21.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:21.666][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:21.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:21.670][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:21.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-25 19:46:21.682][biodb::testContext]
biodb.INFO [2025-03-25 19:46:21.683][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-25 19:46:21.685][biodb::testContext] Test context - Test retrieval of entries
biodb.INFO [2025-03-25 19:46:21.686][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-25 19:46:21.688][biodb::testContext]
biodb.INFO [2025-03-25 19:46:21.701][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-25 19:46:21.704][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-25 19:46:21.717][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-25 19:46:21.719][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-25 19:46:21.720][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-25 19:46:21.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:21.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:21.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:21.732][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-25 19:46:21.734][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-25 19:46:21.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:21.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:21.738][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[2025-03-25 19:46:21.739][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-25 19:46:21.746][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-25 19:46:21.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:21.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:21.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:21.754][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-25 19:46:21.756][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-25 19:46:21.763][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-25 19:46:21.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:21.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:21.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:21.770][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-25 19:46:21.772][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-25 19:46:21.782][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-25 19:46:21.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:21.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:21.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:21.789][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-25 19:46:21.790][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-25 19:46:21.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:21.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:21.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:21.802][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-25 19:46:21.804][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-25 19:46:21.806][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-25 19:46:21.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:21.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:21.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:21.819][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-25 19:46:21.820][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-25 19:46:21.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:21.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:21.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:21.832][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-25 19:46:21.833][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-25 19:46:21.835][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-25 19:46:21.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:21.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:21.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:21.849][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-25 19:46:21.852][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-25 19:46:21.854][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-25 19:46:21.856][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-25 19:46:21.858][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-25 19:46:21.860][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-25 19:46:21.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:21.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:21.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:21.871][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-25 19:46:21.873][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-25 19:46:21.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:21.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:21.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:21.886][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-25 19:46:21.887][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-25 19:46:21.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:21.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:21.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:21.900][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-25 19:46:21.901][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-25 19:46:21.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:21.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:21.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:21.923][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-25 19:46:21.933][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-25 19:46:21.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:21.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:21.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:21.938][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-25 19:46:21.940][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-25 19:46:21.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:21.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:21.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:21.951][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-25 19:46:21.953][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-25 19:46:21.990][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-25 19:46:21.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:21.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:21.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:21.996][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-25 19:46:21.997][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-25 19:46:21.999][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-25 19:46:22.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:22.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:22.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:22.005][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-25 19:46:22.007][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:22.009][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-25 19:46:22.010][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:22.011][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-25 19:46:22.013][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:22.014][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-25 19:46:22.016][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:22.017][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-25 19:46:22.019][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-25 19:46:22.029][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-25 19:46:22.031][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:22.033][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-25 19:46:22.034][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-25 19:46:22.036][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:22.046][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:22.048][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-25 19:46:22.048][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-25 19:46:22.048][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-25 19:46:22.048][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-25 19:46:22.048][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-25 19:46:22.051][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-25 19:46:22.052][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:46:22.054][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:46:22.061][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-25 19:46:22.063][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:46:22.065][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:46:22.066][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-25 19:46:22.068][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:22.074][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-25 19:46:22.076][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-25 19:46:22.078][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:22.080][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:22.082][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-25 19:46:22.091][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:22.093][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-25 19:46:22.095][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:22.097][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-25 19:46:22.108][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:22.110][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-25 19:46:22.112][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:22.114][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-25 19:46:22.116][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-25 19:46:22.126][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-25 19:46:22.128][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:22.130][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-25 19:46:22.132][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-25 19:46:22.134][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:22.144][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:22.147][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-25 19:46:22.147][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-25 19:46:22.147][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-25 19:46:22.147][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-25 19:46:22.147][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-25 19:46:22.149][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-25 19:46:22.151][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:46:22.152][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:46:22.163][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-25 19:46:22.165][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:46:22.169][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:46:22.171][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-25 19:46:22.173][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:22.182][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-25 19:46:22.183][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-25 19:46:22.185][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:22.187][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:22.190][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-25 19:46:22.193][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:22.194][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-25 19:46:22.196][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:22.203][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-25 19:46:22.205][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:22.206][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-25 19:46:22.208][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:22.210][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-25 19:46:22.220][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-25 19:46:22.224][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-25 19:46:22.226][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:22.228][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-25 19:46:22.230][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-25 19:46:22.238][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:22.241][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:22.243][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:22.246][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-25 19:46:22.257][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:46:22.259][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:46:22.261][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-25 19:46:22.263][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:46:22.265][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:46:22.292][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-25 19:46:22.294][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:22.297][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-25 19:46:22.299][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-25 19:46:22.307][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:22.309][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:22.311][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-25 19:46:22.313][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:22.320][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-25 19:46:22.322][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:22.324][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-25 19:46:22.325][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:22.327][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-25 19:46:22.328][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:22.339][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-25 19:46:22.342][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-25 19:46:22.344][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-25 19:46:22.345][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:22.347][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-25 19:46:22.349][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-25 19:46:22.356][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:22.358][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:22.360][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:22.362][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-25 19:46:22.364][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:46:22.366][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:46:22.374][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-25 19:46:22.377][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:46:22.379][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:46:22.381][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-25 19:46:22.383][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:22.385][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-25 19:46:22.396][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-25 19:46:22.398][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:22.400][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:22.402][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-25 19:46:22.403][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:22.404][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[2025-03-25 19:46:22.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:22.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:22.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:22.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:22.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:22.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:22.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:22.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:22.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:22.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:22.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:22.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:22.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:22.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:22.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:22.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:22.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:22.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:22.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:22.464][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[2025-03-25 19:46:22.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:22.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:22.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:22.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:22.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:22.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:22.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:22.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:22.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:22.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:22.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:22.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:22.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:22.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:22.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:22.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:22.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:22.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:22.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:22.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:22.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:22.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:22.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:22.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:22.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:22.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:22.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:22.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:22.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:22.558][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[2025-03-25 19:46:22.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:22.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:22.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:22.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:22.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:22.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:22.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:22.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:22.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:22.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:22.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:22.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:22.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:22.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:22.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:22.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:22.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:22.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:22.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:22.626][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[2025-03-25 19:46:22.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:22.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:22.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:22.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:22.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:22.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:22.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:22.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:22.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:22.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:22.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:22.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:22.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:22.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:22.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:22.696][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-25 19:46:22.708][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-25 19:46:22.711][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-25 19:46:22.713][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-25 19:46:22.724][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-25 19:46:22.727][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-25 19:46:22.730][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-25 19:46:22.732][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-25 19:46:22.743][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-25 19:46:22.746][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-25 19:46:22.748][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-25 19:46:22.759][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-25 19:46:22.762][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-25 19:46:22.765][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-25 19:46:22.767][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-25 19:46:22.778][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-25 19:46:22.780][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-25 19:46:22.783][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-25 19:46:22.793][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-25 19:46:22.796][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-25 19:46:22.799][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-25 19:46:22.801][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-25 19:46:22.811][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-25 19:46:22.815][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-25 19:46:22.818][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-25 19:46:22.831][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-25 19:46:22.834][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-25 19:46:22.838][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-25 19:46:22.846][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-25 19:46:22.849][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-25 19:46:22.852][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-25 19:46:22.864][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-25 19:46:22.867][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-25 19:46:22.871][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-25 19:46:22.882][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-25 19:46:22.886][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-25 19:46:22.889][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-25 19:46:22.902][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-25 19:46:22.906][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-25 19:46:22.912][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-25 19:46:22.923][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-25 19:46:22.927][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-25 19:46:22.939][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-25 19:46:22.943][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-25 19:46:22.946][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-25 19:46:22.956][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-25 19:46:22.959][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-25 19:46:22.963][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-25 19:46:22.975][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-25 19:46:23.000][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-25 19:46:23.003][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-25 19:46:23.006][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-25 19:46:23.009][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-25 19:46:23.012][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-25 19:46:23.019][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-25 19:46:23.024][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-25 19:46:23.026][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-25 19:46:23.035][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-25 19:46:23.038][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-25 19:46:23.040][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-25 19:46:23.043][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-25 19:46:23.052][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-25 19:46:23.055][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-25 19:46:23.058][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-25 19:46:23.069][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-25 19:46:23.098][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-25 19:46:23.103][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-25 19:46:23.117][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-25 19:46:23.122][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-25 19:46:23.126][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-25 19:46:23.138][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-25 19:46:23.142][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-25 19:46:23.153][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-25 19:46:23.157][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-25 19:46:23.161][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-25 19:46:23.173][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-25 19:46:23.186][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-25 19:46:23.189][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-25 19:46:23.191][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-25 19:46:23.193][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-25 19:46:23.204][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-25 19:46:23.209][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-25 19:46:23.215][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-25 19:46:23.217][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-25 19:46:23.220][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-25 19:46:23.221][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-25 19:46:23.223][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:23.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:23.225][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:23.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:23.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:23.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:23.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:23.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:23.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:23.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:23.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:23.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:23.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:23.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:23.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:23.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:23.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:23.263][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[2025-03-25 19:46:23.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:23.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:23.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:23.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:23.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:23.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:23.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:23.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:23.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:23.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:23.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:23.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:23.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:23.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:23.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:23.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:23.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:23.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:23.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:23.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:23.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:23.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:23.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:23.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:23.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:23.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:23.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:23.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:23.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:23.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:23.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:23.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:23.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:23.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:23.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:23.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:23.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:23.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:23.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:23.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:23.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:23.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:23.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:23.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:23.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:23.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:23.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:23.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:23.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:23.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:23.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:23.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:23.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:23.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:23.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:23.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:23.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:23.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:23.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:23.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:23.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:23.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:23.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:23.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:23.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:23.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:23.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:23.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:23.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:23.450][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[2025-03-25 19:46:23.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:23.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:23.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:23.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:23.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:23.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:23.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:23.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:23.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:23.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:23.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:23.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:23.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:23.485][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[2025-03-25 19:46:23.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:23.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:23.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:23.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:23.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:23.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:23.503][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[2025-03-25 19:46:23.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:23.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:23.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:23.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:23.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:23.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:23.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:23.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:23.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:23.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:23.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:23.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:23.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:23.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:23.565][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-03-25 19:46:23.567][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-03-25 19:46:23.570][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:23.572][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-25 19:46:23.573][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:23.575][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-25 19:46:23.576][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:23.579][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-03-25 19:46:23.583][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:23.586][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-25 19:46:23.588][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-25 19:46:23.589][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-25 19:46:23.591][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:23.593][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-03-25 19:46:23.594][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-25 19:46:23.603][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-03-25 19:46:23.603][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-03-25 19:46:23.603][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-03-25 19:46:23.603][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-03-25 19:46:23.603][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-03-25 19:46:23.603][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-03-25 19:46:23.603][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-03-25 19:46:23.603][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-03-25 19:46:23.603][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-03-25 19:46:23.603][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-03-25 19:46:23.603][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-03-25 19:46:23.603][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-03-25 19:46:23.603][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-03-25 19:46:23.603][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-03-25 19:46:23.603][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-03-25 19:46:23.603][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-03-25 19:46:23.603][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-03-25 19:46:23.603][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-03-25 19:46:23.605][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:23.607][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-25 19:46:23.607][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-03-25 19:46:23.607][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-03-25 19:46:23.609][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-25 19:46:23.610][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:46:23.612][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:46:23.620][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-25 19:46:23.621][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:46:23.623][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:46:23.624][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-25 19:46:23.626][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-03-25 19:46:23.626][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-03-25 19:46:23.627][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-25 19:46:23.628][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-25 19:46:23.636][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:23.638][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:23.640][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-03-25 19:46:23.642][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-25 19:46:23.652][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-25 19:46:23.655][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-25 19:46:23.657][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-25 19:46:23.661][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-03-25 19:46:23.668][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-03-25 19:46:23.670][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-03-25 19:46:23.672][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-25 19:46:23.674][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-25 19:46:23.676][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-25 19:46:23.685][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-03-25 19:46:23.687][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2025-03-25 19:46:23.689][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-03-25 19:46:23.689][self$setPropertyValue] Setting property "urls" to "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2025-03-25 19:46:23.691][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-25 19:46:23.692][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-25 19:46:23.693][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2025-03-25 19:46:23.700][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2025-03-25 19:46:23.702][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2025-03-25 19:46:23.704][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-25 19:46:23.706][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-25 19:46:23.708][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-25 19:46:23.716][private$addConnectorRules] Create new rule for URL "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-25 19:46:23.718][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-25 19:46:23.720][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2025-03-25 19:46:23.722][biodb::testThat]
biodb.INFO [2025-03-25 19:46:23.723][biodb::testThat] Running test function  test.hmdbmetabolite.nbentries  (" HMDB metabolite returns enough entries. ").
biodb.INFO [2025-03-25 19:46:23.725][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-25 19:46:23.758][biodb::testThat]
biodb.DEBUG[2025-03-25 19:46:23.764][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:46:23.767][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:46:23.769][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-25 19:46:23.771][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:46:23.774][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-25 19:46:23.778][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-25 19:46:23.779][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-25 19:46:23.781][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-25 19:46:23.782][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-25 19:46:23.791][conn$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-03-25 19:46:23.813][biodb::testThat]
biodb.INFO [2025-03-25 19:46:23.815][biodb::testThat] Running test function  test.old.accession  (" We can retrieve entries using old accession numbers. ").
biodb.INFO [2025-03-25 19:46:23.816][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-25 19:46:23.817][biodb::testThat]
biodb.DEBUG[2025-03-25 19:46:23.820][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2025-03-25 19:46:23.826][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-03-25 19:46:23.829][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:46:23.831][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-03-25 19:46:23.834][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2025-03-25 19:46:23.844][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-25 19:46:23.847][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2025-03-25 19:46:23.849][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-03-25 19:46:23.851][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-25 19:46:23.853][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-25 19:46:23.856][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-25 19:46:23.867][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:23.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:23.882][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:23.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:23.885][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:23.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-25 19:46:23.901][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:23.903][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:23.904][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:23.906][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:23.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:23.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:23.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:23.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:23.938][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:23.940][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:23.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:23.943][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:23.945][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:23.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:23.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:23.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:23.966][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:46:23.968][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:46:23.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:23.974][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:23.977][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:46:23.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:46:23.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:23.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:23.983][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:46:23.992][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:46:23.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:23.995][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:23.997][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:46:23.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:46:24.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.004][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:46:24.006][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:46:24.007][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.020][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:46:24.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:46:24.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.030][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:24.037][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:24.038][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.040][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.042][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:24.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:24.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.049][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:24.050][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:24.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.052][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.054][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:24.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:24.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.066][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:24.068][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:24.070][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.071][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.073][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:24.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:24.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.077][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:24.078][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:24.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.099][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.100][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:24.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:24.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.105][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:24.106][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:24.107][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.109][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.111][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:24.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:24.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.120][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:46:24.121][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:46:24.122][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.123][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.137][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:46:24.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:46:24.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.143][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:46:24.144][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:46:24.146][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.147][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.148][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:46:24.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:46:24.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.152][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:46:24.154][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:24.155][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.157][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.158][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:46:24.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:24.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.164][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:24.165][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:24.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.166][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.169][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:24.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:24.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.176][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:24.177][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:24.184][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.185][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.187][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:24.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:24.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.250][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:24.256][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:24.258][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.263][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.266][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:24.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:24.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.276][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:46:24.277][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:46:24.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.281][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.283][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:46:24.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:46:24.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.290][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-03-25 19:46:24.302][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:46:24.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.306][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.308][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-03-25 19:46:24.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:46:24.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:24.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:24.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:24.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:24.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:24.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:24.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.334][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:46:24.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:46:24.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.351][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:46:24.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:46:24.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.357][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:46:24.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:46:24.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.362][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:46:24.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:46:24.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.367][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:46:24.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:46:24.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.373][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:46:24.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:46:24.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.397][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:46:24.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:46:24.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:46:24.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:46:24.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.418][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:46:24.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:46:24.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:24.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:24.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:24.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:24.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.435][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:24.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:24.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.440][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:24.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:24.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.449][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:24.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:24.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.455][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:24.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:24.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.461][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:24.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:24.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.467][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:24.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:24.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.474][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:24.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:24.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.479][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-25 19:46:24.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:46:24.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.490][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-25 19:46:24.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:46:24.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.495][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-25 19:46:24.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:46:24.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.503][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:24.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:24.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.507][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:24.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:24.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.511][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:24.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:24.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.537][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:46:24.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:46:24.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.543][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:46:24.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:46:24.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.563][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:46:24.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:46:24.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.574][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:46:24.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:46:24.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.580][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:46:24.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:46:24.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.586][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:46:24.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:46:24.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.593][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:46:24.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:24.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.598][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:46:24.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:24.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.606][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:46:24.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:24.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.616][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:24.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:24.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.627][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:24.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:24.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.635][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:24.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:24.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.641][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:24.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:24.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.645][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:24.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:24.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.649][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:24.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:24.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.685][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:24.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:24.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.694][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:24.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:24.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.705][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:24.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:24.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.711][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:24.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:24.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.722][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:24.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:24.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.730][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:24.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:24.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.736][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:24.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:24.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.747][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:24.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:24.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.757][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:24.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:24.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.771][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:46:24.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:46:24.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.783][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:46:24.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:46:24.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.793][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:46:24.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:46:24.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.800][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-25 19:46:24.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:24.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.851][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:46:24.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:24.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.864][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:46:24.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:24.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.895][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:46:24.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:24.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.900][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-25 19:46:24.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:24.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.907][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:24.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:24.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.918][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:24.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:24.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.924][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:24.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:24.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.936][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:24.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:24.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.942][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:24.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:24.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.960][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:46:24.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:46:24.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.973][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:46:24.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:46:24.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:24.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:24.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:24.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:24.994][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:46:24.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:46:24.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:25.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:25.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:25.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:25.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:25.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:25.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:25.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:25.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:25.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:25.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:25.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:25.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:25.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:25.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:25.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:25.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:25.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:25.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:25.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:25.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:25.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:25.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:25.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:25.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:25.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-25 19:46:25.070][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2025-03-25 19:46:25.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:25.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:25.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:25.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:25.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:25.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:25.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:25.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:25.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:25.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:25.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:25.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-25 19:46:25.126][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-25 19:46:25.128][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-03-25 19:46:25.129][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-03-25 19:46:25.131][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-25 19:46:25.132][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:25.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:25.143][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:25.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:25.172][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-25 19:46:25.188][biodb::testContext]
biodb.INFO [2025-03-25 19:46:25.190][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-25 19:46:25.191][biodb::testContext] Test context - Test search of entries
biodb.INFO [2025-03-25 19:46:25.193][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-25 19:46:25.194][biodb::testContext]
biodb.INFO [2025-03-25 19:46:25.209][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-25 19:46:25.212][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-25 19:46:25.229][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-25 19:46:25.231][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-25 19:46:25.233][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-25 19:46:25.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.244][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-25 19:46:25.246][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-25 19:46:25.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.251][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-25 19:46:25.262][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-25 19:46:25.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.268][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-25 19:46:25.269][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-25 19:46:25.270][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-25 19:46:25.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.290][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-25 19:46:25.291][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-25 19:46:25.293][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-25 19:46:25.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.307][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-25 19:46:25.309][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-25 19:46:25.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.323][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-25 19:46:25.325][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-25 19:46:25.327][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-25 19:46:25.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.340][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-25 19:46:25.342][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-25 19:46:25.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.347][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-25 19:46:25.356][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-25 19:46:25.358][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-25 19:46:25.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.364][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-25 19:46:25.365][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-25 19:46:25.373][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-25 19:46:25.375][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-25 19:46:25.376][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-25 19:46:25.378][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-25 19:46:25.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.394][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-25 19:46:25.398][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-25 19:46:25.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.405][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-25 19:46:25.418][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-25 19:46:25.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.425][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-25 19:46:25.426][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-25 19:46:25.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.436][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[2025-03-25 19:46:25.437][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-25 19:46:25.439][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-25 19:46:25.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.448][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-25 19:46:25.450][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-25 19:46:25.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.455][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-25 19:46:25.457][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-25 19:46:25.495][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-25 19:46:25.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.500][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-25 19:46:25.501][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-25 19:46:25.511][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-25 19:46:25.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.516][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[2025-03-25 19:46:25.518][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-25 19:46:25.520][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:25.522][self$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[2025-03-25 19:46:25.526][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:25.527][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-25 19:46:25.529][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:25.531][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-25 19:46:25.532][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:25.533][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-25 19:46:25.535][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-25 19:46:25.545][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-25 19:46:25.547][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:25.549][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-25 19:46:25.551][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-25 19:46:25.552][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:25.553][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:25.556][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-25 19:46:25.556][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-25 19:46:25.556][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-25 19:46:25.556][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-25 19:46:25.556][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-25 19:46:25.563][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-25 19:46:25.565][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:46:25.567][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:46:25.568][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-25 19:46:25.570][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:46:25.571][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:46:25.573][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-25 19:46:25.575][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:25.576][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-25 19:46:25.577][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-25 19:46:25.579][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:25.580][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:25.582][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-25 19:46:25.585][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:25.587][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-25 19:46:25.589][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:25.590][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-25 19:46:25.591][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:25.593][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-25 19:46:25.594][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:25.595][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-25 19:46:25.605][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-25 19:46:25.607][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-25 19:46:25.608][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:25.610][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-25 19:46:25.611][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-25 19:46:25.612][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:25.614][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:25.621][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-25 19:46:25.621][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-25 19:46:25.621][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-25 19:46:25.621][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-25 19:46:25.621][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-25 19:46:25.623][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-25 19:46:25.624][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:46:25.626][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:46:25.627][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-25 19:46:25.629][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:46:25.632][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:46:25.634][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-25 19:46:25.635][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:25.636][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-25 19:46:25.638][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-25 19:46:25.639][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:25.640][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:25.642][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-25 19:46:25.647][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:25.648][self$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[2025-03-25 19:46:25.650][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:25.651][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-25 19:46:25.653][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:25.654][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-25 19:46:25.655][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:25.657][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-25 19:46:25.658][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-25 19:46:25.659][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-25 19:46:25.661][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:25.662][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-25 19:46:25.664][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-25 19:46:25.665][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:25.666][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:25.668][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:25.669][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-25 19:46:25.670][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:46:25.671][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:46:25.673][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-25 19:46:25.674][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:46:25.675][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:46:25.677][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-25 19:46:25.678][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:25.680][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-25 19:46:25.681][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-25 19:46:25.682][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:25.684][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:25.685][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-25 19:46:25.693][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:25.696][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-25 19:46:25.698][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:25.700][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-25 19:46:25.701][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:25.703][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-25 19:46:25.705][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:25.715][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-25 19:46:25.717][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-25 19:46:25.719][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-25 19:46:25.721][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:25.722][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-25 19:46:25.725][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-25 19:46:25.727][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:25.729][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:25.730][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:25.731][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-25 19:46:25.733][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:46:25.734][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:46:25.735][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-25 19:46:25.737][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:46:25.738][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:46:25.740][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-25 19:46:25.741][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:25.742][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-25 19:46:25.744][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-25 19:46:25.745][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:25.746][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:25.748][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-25 19:46:25.749][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:25.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:25.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:25.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:25.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.766][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[2025-03-25 19:46:25.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:25.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:25.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:25.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:25.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:25.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:25.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:25.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:25.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:25.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:25.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:25.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:25.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:25.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:25.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.829][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.DEBUG[2025-03-25 19:46:25.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:25.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:25.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:25.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:25.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:25.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:25.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:25.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:25.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:25.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:25.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:25.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:25.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:25.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:25.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:25.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:25.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:25.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:25.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:25.893][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-25 19:46:25.896][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-25 19:46:25.899][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-25 19:46:25.904][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-25 19:46:25.906][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-25 19:46:25.909][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-25 19:46:25.911][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-25 19:46:25.915][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-25 19:46:25.918][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-25 19:46:25.920][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-25 19:46:25.922][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-25 19:46:25.924][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-25 19:46:25.948][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-25 19:46:25.951][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-25 19:46:25.953][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-25 19:46:25.956][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-25 19:46:25.960][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-25 19:46:25.963][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-25 19:46:25.966][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-25 19:46:25.969][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-25 19:46:25.976][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-25 19:46:25.978][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-25 19:46:25.980][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-25 19:46:25.983][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-25 19:46:25.985][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-25 19:46:25.988][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-25 19:46:25.990][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-25 19:46:25.992][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-25 19:46:25.994][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-25 19:46:25.998][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-25 19:46:26.000][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-25 19:46:26.002][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-25 19:46:26.004][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-25 19:46:26.006][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-25 19:46:26.014][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-25 19:46:26.017][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-25 19:46:26.019][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-25 19:46:26.021][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-25 19:46:26.023][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-25 19:46:26.026][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-25 19:46:26.028][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-25 19:46:26.030][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-25 19:46:26.032][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-25 19:46:26.034][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-25 19:46:26.042][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-25 19:46:26.045][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-25 19:46:26.047][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-25 19:46:26.050][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-25 19:46:26.060][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-25 19:46:26.063][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-25 19:46:26.065][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-25 19:46:26.068][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-25 19:46:26.072][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-25 19:46:26.074][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-25 19:46:26.076][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-25 19:46:26.078][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-25 19:46:26.079][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-25 19:46:26.080][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-25 19:46:26.081][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-25 19:46:26.083][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-25 19:46:26.094][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-25 19:46:26.096][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-25 19:46:26.097][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-25 19:46:26.098][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-25 19:46:26.099][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-25 19:46:26.100][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-25 19:46:26.101][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-25 19:46:26.103][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-25 19:46:26.104][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-25 19:46:26.105][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-25 19:46:26.110][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-25 19:46:26.112][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-25 19:46:26.113][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-25 19:46:26.114][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-25 19:46:26.115][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-25 19:46:26.117][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-25 19:46:26.118][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-25 19:46:26.119][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-25 19:46:26.120][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-25 19:46:26.121][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-25 19:46:26.122][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-25 19:46:26.123][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-25 19:46:26.124][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-25 19:46:26.125][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-25 19:46:26.210][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-25 19:46:26.211][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-25 19:46:26.212][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:26.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:26.214][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:26.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:26.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:26.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:26.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:26.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:26.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:26.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:26.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:26.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:26.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:26.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:26.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:26.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:26.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:26.225][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[2025-03-25 19:46:26.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:26.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:26.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:26.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:26.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:26.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:26.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:26.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:26.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:26.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:26.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:26.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:26.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:26.246][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[2025-03-25 19:46:26.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:26.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:26.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:26.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:26.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:26.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:26.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:26.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:26.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:26.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:26.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:26.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:26.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:26.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:26.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:26.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:26.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:26.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:26.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:26.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:26.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:26.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:26.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:26.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:26.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:26.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:26.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:26.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:26.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:26.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:26.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:26.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:26.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:26.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:26.321][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[2025-03-25 19:46:26.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:26.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:26.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:26.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:26.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:26.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:26.326][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[2025-03-25 19:46:26.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:26.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:26.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:26.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:26.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:26.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:26.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:26.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:26.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:26.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:26.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:26.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:26.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:26.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:26.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:26.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:26.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:26.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:26.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:26.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:26.436][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[2025-03-25 19:46:26.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:26.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:26.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:26.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:26.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:26.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:26.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:26.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:26.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:26.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:26.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:26.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:26.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:26.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:26.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:26.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:26.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:26.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:26.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:26.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:26.450][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[2025-03-25 19:46:26.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-25 19:46:26.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:26.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:26.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:26.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:26.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:26.466][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[2025-03-25 19:46:26.469][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-03-25 19:46:26.471][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-03-25 19:46:26.472][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:26.528][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-25 19:46:26.529][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:26.530][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-25 19:46:26.531][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:26.532][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-03-25 19:46:26.533][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:26.534][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-25 19:46:26.534][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-25 19:46:26.535][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-25 19:46:26.536][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:26.537][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-03-25 19:46:26.537][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-25 19:46:26.538][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-03-25 19:46:26.538][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-03-25 19:46:26.538][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-03-25 19:46:26.538][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-03-25 19:46:26.538][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-03-25 19:46:26.538][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-03-25 19:46:26.538][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-03-25 19:46:26.538][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-03-25 19:46:26.538][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-03-25 19:46:26.538][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-03-25 19:46:26.538][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-03-25 19:46:26.538][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-03-25 19:46:26.538][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-03-25 19:46:26.538][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-03-25 19:46:26.538][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-03-25 19:46:26.538][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-03-25 19:46:26.538][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-03-25 19:46:26.538][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-03-25 19:46:26.540][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-25 19:46:26.540][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-25 19:46:26.540][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-03-25 19:46:26.540][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-03-25 19:46:26.541][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-25 19:46:26.542][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:46:26.543][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:46:26.543][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-25 19:46:26.544][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-25 19:46:26.545][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-25 19:46:26.556][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-25 19:46:26.557][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-03-25 19:46:26.557][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-03-25 19:46:26.589][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-25 19:46:26.590][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-25 19:46:26.591][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-25 19:46:26.591][self$setPropertyValue]
biodb.DEBUG[2025-03-25 19:46:26.592][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-03-25 19:46:26.594][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-25 19:46:26.595][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-25 19:46:26.597][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-25 19:46:26.598][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-25 19:46:26.616][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-03-25 19:46:26.617][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-03-25 19:46:26.618][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-03-25 19:46:26.620][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-25 19:46:26.621][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-25 19:46:26.621][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-25 19:46:26.623][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-03-25 19:46:26.623][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2025-03-25 19:46:26.624][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-03-25 19:46:26.624][self$setPropertyValue] Setting property "urls" to "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2025-03-25 19:46:26.625][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-25 19:46:26.626][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-25 19:46:26.627][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2025-03-25 19:46:26.627][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2025-03-25 19:46:26.629][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2025-03-25 19:46:26.630][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-25 19:46:26.631][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-25 19:46:26.632][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-25 19:46:26.633][private$addConnectorRules] Create new rule for URL "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2025-03-25 19:46:26.655][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-25 19:46:26.667][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2025-03-25 19:46:26.668][biodb::testThat]
biodb.INFO [2025-03-25 19:46:26.669][biodb::testThat] Running test function  test.searchMultipleWordsInDescription  (" We can search for multiple words inside description field. ").
biodb.INFO [2025-03-25 19:46:26.670][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-25 19:46:26.675][biodb::testThat]
biodb.DEBUG[2025-03-25 19:46:26.677][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-03-25 19:46:26.678][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2025-03-25 19:46:26.679][private$doSearchForEntries] fields VALUES = and
biodb.INFO [2025-03-25 19:46:26.681][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2025-03-25 19:46:26.683][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2025-03-25 19:46:26.683][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2025-03-25 19:46:26.684][private$doDownload] Downloading HMDB metabolite database at "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" ...
biodb.TRACE[2025-03-25 19:46:26.686][cch$addFilesToCache] Moving files to cache [1]: "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.TRACE[2025-03-25 19:46:26.697][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2025-03-25 19:46:26.701][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2025-03-25 19:46:26.702][self$getDownloadPath] Download path of hmdb.metabolites is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2025-03-25 19:46:26.703][self$download] Downloading of hmdb.metabolites completed.
biodb.TRACE[2025-03-25 19:46:26.716][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker143fd65529b36marker".
biodb.TRACE[2025-03-25 19:46:26.717][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/downloaded.marker".
biodb.DEBUG[2025-03-25 19:46:26.718][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-03-25 19:46:26.719][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2025-03-25 19:46:26.720][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2025-03-25 19:46:26.721][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.DEBUG[2025-03-25 19:46:26.722][self$getDownloadPath] Download path of hmdb.metabolites is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2025-03-25 19:46:26.723][private$doExtractDownload] Unzipping /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp...
biodb.DEBUG[2025-03-25 19:46:26.746][private$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[2025-03-25 19:46:26.747][private$findXmlDatabaseFile] Found XML file /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/hmdb_two_full_entries.xml in ZIP file.
biodb.DEBUG[2025-03-25 19:46:26.747][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2025-03-25 19:46:26.749][private$doExtractDownload] Extract entries from XML file "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/hmdb_two_full_entries.xml", into "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp".
biodb.TRACE[2025-03-25 19:46:26.845][self$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[2025-03-25 19:46:26.846][private$doAddFilesToCache] Destination files are [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2025-03-25 19:46:26.847][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-03-25 19:46:26.848][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2025-03-25 19:46:26.850][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker143fd124c2a32marker".
biodb.TRACE[2025-03-25 19:46:26.851][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/extracted.marker".
biodb.DEBUG[2025-03-25 19:46:26.852][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-03-25 19:46:26.853][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-25 19:46:26.854][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:46:26.866][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-25 19:46:26.867][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-25 19:46:26.868][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-25 19:46:26.869][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-25 19:46:26.870][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-25 19:46:26.881][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-25 19:46:26.882][private$doSearchForEntries] Total number of IDs = 2
biodb.DEBUG[2025-03-25 19:46:26.883][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-03-25 19:46:26.884][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-03-25 19:46:26.895][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:46:26.923][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-03-25 19:46:26.940][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2025-03-25 19:46:26.952][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-25 19:46:26.954][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2025-03-25 19:46:26.955][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-03-25 19:46:26.966][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-25 19:46:26.967][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-25 19:46:26.969][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-25 19:46:26.969][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:26.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:26.975][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:26.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:26.987][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:26.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-25 19:46:27.411][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:27.412][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:27.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.413][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:27.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:27.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.417][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:27.418][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:27.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.420][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.421][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:27.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:27.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.424][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:46:27.425][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:46:27.426][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.427][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.428][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:46:27.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:46:27.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.432][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:46:27.433][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:46:27.434][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.435][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.441][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:46:27.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:46:27.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.445][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:46:27.446][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:46:27.447][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.447][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.448][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:46:27.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:46:27.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.452][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:27.453][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:27.453][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.454][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.456][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:27.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:27.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.459][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:27.460][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:27.460][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.461][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.462][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:27.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:27.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.466][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:27.467][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:27.467][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.468][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.469][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:27.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:27.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.472][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:27.473][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:27.474][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.475][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.476][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:27.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:27.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.479][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:27.480][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:27.481][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.482][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.483][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:27.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:27.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.486][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:46:27.487][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:46:27.488][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.489][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.501][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:46:27.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:46:27.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.504][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:46:27.505][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:46:27.506][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.506][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.520][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:46:27.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:46:27.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.523][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:46:27.524][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:27.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.525][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.526][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:46:27.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:27.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.530][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:27.531][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:27.533][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.534][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.536][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:27.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:27.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.543][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:27.544][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:27.546][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.547][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.559][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:27.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:27.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.585][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:27.586][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:27.587][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.588][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.589][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:27.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:27.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.603][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:46:27.604][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:46:27.605][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.606][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.607][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:46:27.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:46:27.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.620][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-03-25 19:46:27.622][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:46:27.623][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.658][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.660][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-03-25 19:46:27.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:46:27.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:27.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:27.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:27.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:27.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:27.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:27.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.716][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:46:27.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:46:27.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.719][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:46:27.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:46:27.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.733][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:46:27.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:46:27.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.736][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:46:27.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:46:27.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.760][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:46:27.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:46:27.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.764][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:46:27.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:46:27.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.768][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:46:27.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:46:27.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.793][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:46:27.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:46:27.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.797][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:46:27.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:46:27.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.800][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:27.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:27.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.943][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:27.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:27.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.950][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:27.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:27.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.961][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:27.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:27.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.976][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:27.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:27.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.982][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:27.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:27.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.990][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:27.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:27.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.994][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:27.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:27.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:27.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:27.997][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:27.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:27.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.005][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-25 19:46:28.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:46:28.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.009][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-25 19:46:28.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:46:28.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.013][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-25 19:46:28.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:46:28.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.038][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:28.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:28.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.041][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:28.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:28.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.044][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:28.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:28.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.047][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:46:28.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:46:28.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.062][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:46:28.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:46:28.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.065][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:46:28.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:46:28.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.068][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:46:28.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:46:28.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.071][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:46:28.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:46:28.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.074][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:46:28.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:46:28.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.078][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:46:28.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:28.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.093][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:46:28.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:28.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.096][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:46:28.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:28.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.099][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:28.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:28.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.112][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:28.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:28.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.116][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:28.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:28.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.119][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:28.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:28.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.144][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:28.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:28.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.147][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:28.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:28.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.151][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:28.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:28.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.175][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:28.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:28.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.178][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:28.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:28.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.191][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:28.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:28.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.195][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:28.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:28.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.202][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:28.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:28.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.206][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:28.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:28.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.219][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:28.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:28.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.223][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:28.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:28.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.226][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:46:28.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:46:28.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.252][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:46:28.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:46:28.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.255][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:46:28.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:46:28.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.258][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-25 19:46:28.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:28.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.261][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:46:28.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:28.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.264][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:46:28.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:28.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.277][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:46:28.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:28.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.281][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-25 19:46:28.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:28.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.296][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:28.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:28.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.299][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:28.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:28.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.302][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:28.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:28.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.305][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:28.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:28.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.516][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:28.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:28.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.704][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:46:28.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:46:28.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.717][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:46:28.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:46:28.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:28.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:28.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.733][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:46:28.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:46:28.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:28.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:28.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:28.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:28.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:28.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:28.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:28.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:28.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:28.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:28.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:28.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:28.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-25 19:46:28.811][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2025-03-25 19:46:28.813][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:28.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:28.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.826][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:28.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:28.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.832][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:28.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:28.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.837][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:28.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:28.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-25 19:46:28.841][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-25 19:46:28.842][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-25 19:46:28.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-25 19:46:28.843][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:28.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:28.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:28.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:28.863][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:28.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:28.876][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2025-03-25 19:46:28.878][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-03-25 19:46:28.880][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:46:28.883][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-03-25 19:46:28.886][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2025-03-25 19:46:28.888][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-25 19:46:28.890][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2025-03-25 19:46:28.891][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-03-25 19:46:28.893][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-03-25 19:46:28.895][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-03-25 19:46:28.897][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-25 19:46:28.898][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:28.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:28.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:28.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:28.909][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:28.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-25 19:46:28.915][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:28.917][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:28.918][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.919][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:28.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:28.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.959][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:28.961][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:28.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.964][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.971][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:28.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:28.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.979][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:46:28.981][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:46:28.982][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.983][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.985][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:46:28.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:46:28.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.989][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:46:28.990][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:46:28.991][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.992][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.993][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:46:28.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:46:28.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:28.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:28.999][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:46:29.001][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:46:29.002][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.002][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.004][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:46:29.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:46:29.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.008][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:29.010][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:29.010][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.012][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:29.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:29.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.022][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:29.024][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:29.025][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.026][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.027][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:29.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:29.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.032][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:29.034][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:29.035][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.036][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.038][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:29.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:29.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.043][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:29.043][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:29.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.045][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.046][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:29.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:29.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.050][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:29.052][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:29.054][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.056][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.057][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:29.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:29.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.061][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:46:29.062][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:46:29.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.085][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.086][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:46:29.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:46:29.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.091][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:46:29.092][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:46:29.093][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.093][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.094][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:46:29.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:46:29.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.098][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:46:29.099][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:29.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.101][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.102][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:46:29.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:29.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.105][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:29.106][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:29.107][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.109][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.111][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:29.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:29.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.117][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:29.118][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:29.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.120][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.122][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:29.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:29.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.126][ef$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:29.127][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:29.128][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.129][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.130][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:29.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:29.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.137][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:46:29.138][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:46:29.139][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.140][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.142][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:46:29.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:46:29.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.147][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-03-25 19:46:29.148][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:46:29.149][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.151][ef$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.153][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-03-25 19:46:29.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:46:29.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:29.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:29.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:29.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:29.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:29.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:29.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.201][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:46:29.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:46:29.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.206][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:46:29.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:46:29.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.211][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-25 19:46:29.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-25 19:46:29.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.217][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:46:29.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:46:29.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.222][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:46:29.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:46:29.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.235][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-25 19:46:29.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-25 19:46:29.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.246][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:46:29.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:46:29.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.252][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:46:29.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:46:29.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-25 19:46:29.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-25 19:46:29.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.265][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:29.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:29.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:29.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:29.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.284][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:29.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-03-25 19:46:29.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.298][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:29.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:29.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.305][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:29.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:29.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.312][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:29.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-03-25 19:46:29.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.317][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:29.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:29.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.323][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:29.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:29.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.328][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:29.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-03-25 19:46:29.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.336][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-25 19:46:29.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:46:29.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.341][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-25 19:46:29.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:46:29.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.347][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-03-25 19:46:29.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-03-25 19:46:29.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.353][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:29.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:29.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.358][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:29.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:29.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.370][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:29.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:29.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.382][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:46:29.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:46:29.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.386][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:46:29.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:46:29.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.389][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-25 19:46:29.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-25 19:46:29.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.393][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:46:29.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:46:29.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.399][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:46:29.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:46:29.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.405][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-25 19:46:29.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-25 19:46:29.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.412][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:46:29.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:29.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.426][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:46:29.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:29.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.432][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:46:29.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:29.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.462][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:29.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:29.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.474][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:29.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:29.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.480][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:29.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-25 19:46:29.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.497][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:29.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:29.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.525][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:29.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:29.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.531][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:29.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-25 19:46:29.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.543][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:29.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:29.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.549][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:29.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:29.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.559][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:29.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:29.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.572][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:29.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:29.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.581][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:29.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:29.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.591][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:29.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-03-25 19:46:29.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.596][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:29.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:29.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.602][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:29.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:29.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.607][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:29.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-03-25 19:46:29.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.622][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:46:29.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:46:29.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.664][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:46:29.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:46:29.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.672][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-25 19:46:29.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-25 19:46:29.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.690][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-25 19:46:29.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:29.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.705][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:46:29.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:29.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.718][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:46:29.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:29.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.724][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-25 19:46:29.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:29.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.737][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-03-25 19:46:29.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-25 19:46:29.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.745][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:29.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:29.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.759][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:29.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:29.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.775][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:29.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:29.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.787][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:29.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:29.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.794][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-25 19:46:29.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-25 19:46:29.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.801][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:46:29.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:46:29.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.810][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:46:29.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:46:29.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:29.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:29.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.830][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:46:29.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-03-25 19:46:29.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:29.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:29.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:29.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:29.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:29.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:29.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:29.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:29.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:29.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:29.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-25 19:46:29.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-25 19:46:29.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-25 19:46:29.908][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2025-03-25 19:46:29.910][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:29.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:29.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.923][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:29.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:29.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.941][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:29.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:29.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:29.955][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:29.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:29.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:29.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-25 19:46:29.997][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-25 19:46:29.999][private$doSearchForEntries] COUNT IDS = 2
biodb.DEBUG[2025-03-25 19:46:30.003][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-25 19:46:30.005][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:30.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:30.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:30.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:30.033][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:30.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:30.054][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-03-25 19:46:30.066][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2025-03-25 19:46:30.068][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2025-03-25 19:46:30.072][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:46:30.083][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:46:30.086][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-25 19:46:30.089][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:46:30.091][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-25 19:46:30.102][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-25 19:46:30.104][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-25 19:46:30.106][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-25 19:46:30.108][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-25 19:46:30.110][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-25 19:46:30.119][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-25 19:46:30.122][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:30.138][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:30.152][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:30.159][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:30.180][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:30.193][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:30.211][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-25 19:46:30.219][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-25 19:46:30.228][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-25 19:46:30.231][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-25 19:46:30.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:30.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:30.248][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:30.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:30.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:30.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-25 19:46:30.254][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:30.268][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:30.295][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:30.312][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:30.326][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:30.334][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:30.349][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-25 19:46:30.372][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2025-03-25 19:46:30.382][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-25 19:46:30.384][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-25 19:46:30.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:30.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:30.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:30.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:30.407][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:30.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-25 19:46:30.431][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-03-25 19:46:30.433][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2025-03-25 19:46:30.435][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2025-03-25 19:46:30.446][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:46:30.449][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:46:30.451][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-03-25 19:46:30.462][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-03-25 19:46:30.465][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-03-25 19:46:30.467][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-03-25 19:46:30.469][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-03-25 19:46:30.471][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-03-25 19:46:30.472][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-03-25 19:46:30.483][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-03-25 19:46:30.487][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-03-25 19:46:30.491][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:30.506][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:30.517][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:30.524][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:30.532][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:30.538][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:30.543][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-25 19:46:30.550][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2025-03-25 19:46:30.551][private$doSearchForEntries] COUNT IDS = 0
biodb.DEBUG[2025-03-25 19:46:30.553][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-25 19:46:30.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:30.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:30.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:30.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:30.566][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:30.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-25 19:46:30.569][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:30.578][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:30.584][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:30.590][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:30.596][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:30.604][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-25 19:46:30.612][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-03-25 19:46:30.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-03-25 19:46:30.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-25 19:46:30.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-25 19:46:30.618][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-03-25 19:46:30.619][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-03-25 19:46:30.628][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-25 19:46:30.647][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:30.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:30.677][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:30.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:30.692][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:30.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-25 19:46:30.735][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-25 19:46:30.738][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-03-25 19:46:30.740][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-03-25 19:46:30.742][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-25 19:46:30.743][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-25 19:46:30.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-25 19:46:30.747][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-25 19:46:30.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-25 19:46:30.750][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-25 19:46:30.751][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 243 ]
> 
> proc.time()
   user  system elapsed 
 11.904   0.753  68.301

CHECK results for biodbHmdb on lconway

Summary

Command output

Installation output

Tests output

Example timings