Multiple platform build/check report for BioC 3.19 - CHECK results for biodbHmdb on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4763
palomino7	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4500
merida1	macOS 12.7.5 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4530
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4480
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 merida1

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: 1.10.2

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_1.10.2.tar.gz

StartedAt: 2024-10-17 01:49:05 -0400 (Thu, 17 Oct 2024)

EndedAt: 2024-10-17 01:51:36 -0400 (Thu, 17 Oct 2024)

EllapsedTime: 150.9 seconds

RetCode: 0

Status: OK

CheckDir: biodbHmdb.Rcheck

Warnings: 0

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_1.10.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbHmdb.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.10.2’
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
HmdbMetabolitesConn 3.962  1.176   6.302
hmdbToSqlite        4.643  0.097   7.371
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbHmdb.Rcheck/00check.log’
for details.

Installation output

biodbHmdb.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘biodbHmdb’ ...
** 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/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/00LOCK-biodbHmdb/00new/biodbHmdb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 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 [2024-10-17 01:51:01.628][biodb::testContext]
biodb.INFO [2024-10-17 01:51:01.636][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 01:51:01.638][biodb::testContext] Test context - Tests of independent functions
biodb.INFO [2024-10-17 01:51:01.644][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 01:51:01.647][biodb::testContext]
biodb.INFO [2024-10-17 01:51:01.650][biodb::testThat]
biodb.INFO [2024-10-17 01:51:01.653][biodb::testThat] Running test function  test_extractXmlEntries  (" extractXmlEntries() works fine. ").
biodb.INFO [2024-10-17 01:51:01.657][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:51:01.660][biodb::testThat]
biodb.INFO [2024-10-17 01:51:01.947][biodb::testContext]
biodb.INFO [2024-10-17 01:51:01.949][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 01:51:01.952][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-10-17 01:51:01.954][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 01:51:01.956][biodb::testContext]
biodb.INFO [2024-10-17 01:51:01.978][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-17 01:51:01.982][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-17 01:51:01.999][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:51:02.001][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-17 01:51:02.004][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-17 01:51:02.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.013][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-17 01:51:02.081][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-17 01:51:02.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.092][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-17 01:51:02.095][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-17 01:51:02.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.104][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-17 01:51:02.106][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-17 01:51:02.108][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-17 01:51:02.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.118][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[2024-10-17 01:51:02.121][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-17 01:51:02.123][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-17 01:51:02.127][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-17 01:51:02.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.135][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-17 01:51:02.137][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-17 01:51:02.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.146][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-17 01:51:02.149][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-17 01:51:02.152][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-17 01:51:02.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.163][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-17 01:51:02.167][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-17 01:51:02.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.177][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-17 01:51:02.180][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-17 01:51:02.183][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-17 01:51:02.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.193][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-17 01:51:02.196][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-17 01:51:02.199][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-17 01:51:02.201][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-17 01:51:02.203][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-17 01:51:02.207][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-17 01:51:02.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.216][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-17 01:51:02.219][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-17 01:51:02.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.229][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-17 01:51:02.232][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-17 01:51:02.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.242][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-17 01:51:02.244][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-17 01:51:02.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.254][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-17 01:51:02.257][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-17 01:51:02.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.267][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-17 01:51:02.270][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-17 01:51:02.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.282][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-17 01:51:02.284][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-17 01:51:02.304][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-17 01:51:02.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.314][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-17 01:51:02.316][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-17 01:51:02.319][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-17 01:51:02.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.332][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-17 01:51:02.432][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:02.497][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-17 01:51:02.499][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:02.502][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:51:02.505][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:02.508][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:51:02.511][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:02.513][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:51:02.518][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 01:51:02.521][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:51:02.524][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:02.526][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-17 01:51:02.529][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:51:02.531][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:02.534][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:02.536][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:51:02.536][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:51:02.536][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 01:51:02.536][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 01:51:02.536][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 01:51:02.540][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:51:02.542][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:02.544][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:02.546][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:51:02.549][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:02.560][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:02.562][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:51:02.565][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:02.567][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:51:02.570][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:51:02.574][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:02.576][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:02.579][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-17 01:51:02.585][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:02.589][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 01:51:02.591][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:02.594][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:51:02.597][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:02.599][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:51:02.602][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:02.604][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:51:02.612][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 01:51:02.614][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:51:02.617][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:02.619][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-17 01:51:02.623][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:51:02.625][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:02.627][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:02.630][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:51:02.630][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:51:02.630][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 01:51:02.630][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 01:51:02.630][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 01:51:02.634][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:51:02.637][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:02.641][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:02.643][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:51:02.645][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:02.651][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:02.653][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:51:02.656][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:02.659][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:51:02.663][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:51:02.666][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:02.668][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:02.671][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-17 01:51:02.679][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:02.682][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-17 01:51:02.684][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:02.689][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:51:02.692][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:02.695][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:51:02.697][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:02.704][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:51:02.707][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 01:51:02.709][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:51:02.712][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:02.715][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-17 01:51:02.719][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:51:02.722][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:02.725][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:02.729][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:02.731][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:51:02.734][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:02.735][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:02.739][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:51:02.742][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:02.744][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:02.746][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:51:02.749][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:02.752][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:51:02.754][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:51:02.757][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:02.760][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:02.763][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-17 01:51:02.768][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:02.771][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 01:51:02.777][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:02.779][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:51:02.781][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:02.783][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:51:02.785][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:02.789][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:51:02.791][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 01:51:02.794][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:51:02.796][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:02.799][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-17 01:51:02.802][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:51:02.805][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:02.808][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:02.813][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:02.815][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:51:02.817][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:02.819][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:02.821][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:51:02.825][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:02.827][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:02.829][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:51:02.832][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:02.835][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:51:02.837][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:51:02.839][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:02.842][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:02.852][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:51:02.854][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:02.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:02.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:02.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:02.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:02.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:02.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:02.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:02.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:02.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:02.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:02.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:02.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:02.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:02.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:02.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:02.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:02.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:02.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:02.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:02.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:02.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:02.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:02.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:02.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:03.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:03.002][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[2024-10-17 01:51:03.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:03.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:03.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:03.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:03.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:03.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:03.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:03.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:03.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:03.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:03.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:03.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:03.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:03.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:03.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:03.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:03.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:03.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:03.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:03.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:03.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:03.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:03.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:03.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:03.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:03.063][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-17 01:51:03.080][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-17 01:51:03.084][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-17 01:51:03.088][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-17 01:51:03.091][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 01:51:03.097][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-17 01:51:03.101][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-17 01:51:03.107][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-17 01:51:03.110][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-17 01:51:03.114][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-17 01:51:03.117][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 01:51:03.122][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-17 01:51:03.125][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-17 01:51:03.129][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-17 01:51:03.135][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-17 01:51:03.139][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 01:51:03.143][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-17 01:51:03.147][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-17 01:51:03.150][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 01:51:03.154][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-17 01:51:03.158][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-17 01:51:03.161][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-17 01:51:03.166][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-17 01:51:03.170][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-17 01:51:03.174][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-17 01:51:03.178][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-17 01:51:03.183][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-17 01:51:03.187][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-17 01:51:03.191][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-17 01:51:03.195][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-17 01:51:03.200][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-17 01:51:03.204][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-17 01:51:03.207][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-17 01:51:03.210][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-17 01:51:03.214][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-17 01:51:03.217][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-17 01:51:03.223][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-17 01:51:03.227][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-17 01:51:03.230][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-17 01:51:03.234][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-17 01:51:03.237][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-17 01:51:03.240][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-17 01:51:03.245][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-17 01:51:03.249][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-17 01:51:03.252][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-17 01:51:03.257][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-17 01:51:03.261][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-17 01:51:03.266][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-17 01:51:03.270][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-17 01:51:03.274][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-17 01:51:03.279][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-17 01:51:03.282][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-17 01:51:03.286][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-17 01:51:03.290][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-17 01:51:03.293][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-17 01:51:03.297][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-17 01:51:03.301][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-17 01:51:03.304][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-17 01:51:03.308][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-17 01:51:03.312][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-17 01:51:03.315][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-17 01:51:03.319][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-17 01:51:03.324][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-17 01:51:03.327][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-17 01:51:03.332][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-17 01:51:03.336][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-17 01:51:03.339][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 01:51:03.343][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 01:51:03.347][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-17 01:51:03.351][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-17 01:51:03.355][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-17 01:51:03.359][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-17 01:51:03.363][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-17 01:51:03.367][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-17 01:51:03.370][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-17 01:51:03.375][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-17 01:51:03.379][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-17 01:51:03.383][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-17 01:51:03.390][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-17 01:51:03.395][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-17 01:51:03.398][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-17 01:51:03.402][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-17 01:51:03.406][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-17 01:51:03.424][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-17 01:51:03.428][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-17 01:51:03.435][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:51:03.437][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:03.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:03.442][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:03.445][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[2024-10-17 01:51:03.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:03.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:03.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:03.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:03.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:03.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:03.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:03.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:03.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:03.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:03.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:03.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:03.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:03.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:03.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:03.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:03.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:03.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:03.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:03.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:03.510][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[2024-10-17 01:51:03.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:03.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:03.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:03.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:03.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:03.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:03.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:03.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:03.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:03.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:03.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:03.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:03.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:03.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:03.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:03.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:03.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:03.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:03.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:03.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:03.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:03.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:03.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:03.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:03.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:03.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:03.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:03.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:03.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:03.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:03.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:03.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:03.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:03.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:03.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:03.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:03.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:03.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:03.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:03.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:03.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:03.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:03.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:03.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:03.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:03.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:03.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:03.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:03.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:03.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:03.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:03.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:03.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:03.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:03.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:03.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:03.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:03.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:03.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:03.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:03.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:03.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:03.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:03.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:03.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:03.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:03.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:03.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:03.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:03.738][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[2024-10-17 01:51:03.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:03.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:03.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:03.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:03.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:03.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:03.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:03.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:03.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:03.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:03.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:03.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:03.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:03.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:03.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:03.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:03.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:03.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:03.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:03.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:03.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:03.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:03.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:03.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:03.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:03.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:03.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:03.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:03.834][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-10-17 01:51:03.871][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-10-17 01:51:03.880][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:03.884][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-17 01:51:03.887][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:03.890][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:51:03.895][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:03.903][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-10-17 01:51:03.906][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:03.908][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:51:03.910][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-17 01:51:03.916][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:51:03.919][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:03.921][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-10-17 01:51:03.924][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:51:03.927][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-10-17 01:51:03.927][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-10-17 01:51:03.927][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-10-17 01:51:03.927][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-10-17 01:51:03.927][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-10-17 01:51:03.927][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-10-17 01:51:03.927][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-10-17 01:51:03.927][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-10-17 01:51:03.927][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-10-17 01:51:03.927][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-10-17 01:51:03.927][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-10-17 01:51:03.927][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-10-17 01:51:03.927][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-10-17 01:51:03.927][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-10-17 01:51:03.927][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-10-17 01:51:03.927][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-10-17 01:51:03.927][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-10-17 01:51:03.927][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-10-17 01:51:03.930][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:03.933][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:51:03.933][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-10-17 01:51:03.933][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-10-17 01:51:03.936][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-17 01:51:03.940][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:03.944][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:03.946][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:51:03.949][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:03.954][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:03.957][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:51:03.959][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-10-17 01:51:03.959][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-10-17 01:51:03.962][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:51:03.965][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:51:03.968][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:03.971][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:03.993][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-10-17 01:51:03.996][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-17 01:51:04.001][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-17 01:51:04.005][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 01:51:04.011][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 01:51:04.069][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-10-17 01:51:04.075][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-10-17 01:51:04.083][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-10-17 01:51:04.094][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-17 01:51:04.107][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 01:51:04.110][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 01:51:04.115][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-10-17 01:51:04.118][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2024-10-17 01:51:04.120][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-10-17 01:51:04.120][self$setPropertyValue] Setting property "urls" to "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2024-10-17 01:51:04.126][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:51:04.128][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:51:04.130][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2024-10-17 01:51:04.133][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2024-10-17 01:51:04.135][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2024-10-17 01:51:04.206][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-17 01:51:04.209][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 01:51:04.212][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 01:51:04.215][private$addConnectorRules] Create new rule for URL "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-17 01:51:04.221][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 01:51:04.225][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2024-10-17 01:51:04.229][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-17 01:51:04.233][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-10-17 01:51:04.261][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-10-17 01:51:04.264][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-17 01:51:04.266][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:04.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:04.272][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:04.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:04.277][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:04.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-17 01:51:04.293][biodb::testContext]
biodb.INFO [2024-10-17 01:51:04.296][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 01:51:04.299][biodb::testContext] Test context - Test retrieval of entries
biodb.INFO [2024-10-17 01:51:04.302][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 01:51:04.305][biodb::testContext]
biodb.INFO [2024-10-17 01:51:04.319][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-17 01:51:04.324][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-17 01:51:04.332][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:51:04.336][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-17 01:51:04.339][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-17 01:51:04.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:04.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:04.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:04.348][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-17 01:51:04.351][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-17 01:51:04.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:04.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:04.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:04.362][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-17 01:51:04.366][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-17 01:51:04.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:04.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:04.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:04.377][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-17 01:51:04.379][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-17 01:51:04.383][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-17 01:51:04.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:04.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:04.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:04.395][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-17 01:51:04.397][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-17 01:51:04.400][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-17 01:51:04.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:04.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:04.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:04.411][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-17 01:51:04.414][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-17 01:51:04.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:04.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:04.423][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[2024-10-17 01:51:04.425][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-17 01:51:04.430][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-17 01:51:04.433][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-17 01:51:04.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:04.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:04.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:04.443][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-17 01:51:04.446][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-17 01:51:04.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:04.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:04.454][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[2024-10-17 01:51:04.456][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-17 01:51:04.458][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-17 01:51:04.462][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-17 01:51:04.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:04.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:04.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:04.471][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-17 01:51:04.474][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-17 01:51:04.476][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-17 01:51:04.479][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-17 01:51:04.482][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-17 01:51:04.484][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-17 01:51:04.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:04.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:04.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:04.494][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-17 01:51:04.497][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-17 01:51:04.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:04.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:04.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:04.507][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-17 01:51:04.509][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-17 01:51:04.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:04.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:04.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:04.521][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-17 01:51:04.524][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-17 01:51:04.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:04.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:04.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:04.534][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-17 01:51:04.538][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-17 01:51:04.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:04.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:04.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:04.547][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-17 01:51:04.551][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-17 01:51:04.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:04.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:04.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:04.561][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-17 01:51:04.563][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-17 01:51:04.586][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-17 01:51:04.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:04.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:04.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:04.598][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-17 01:51:04.601][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-17 01:51:04.603][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-17 01:51:04.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:04.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:04.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:04.616][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-17 01:51:04.621][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:04.624][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-17 01:51:04.628][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:04.631][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:51:04.636][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:04.639][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:51:04.643][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:04.646][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:51:04.649][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 01:51:04.652][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:51:04.654][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:04.659][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-17 01:51:04.662][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:51:04.664][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:04.667][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:04.671][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:51:04.671][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:51:04.671][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 01:51:04.671][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 01:51:04.671][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 01:51:04.674][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:51:04.677][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:04.688][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:04.691][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:51:04.694][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:04.696][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:04.699][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:51:04.702][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:04.704][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:51:04.706][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:51:04.709][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:04.712][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:04.716][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-17 01:51:04.721][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:04.726][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 01:51:04.728][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:04.731][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:51:04.734][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:04.738][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:51:04.741][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:04.743][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:51:04.747][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 01:51:04.751][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:51:04.753][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:04.756][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-17 01:51:04.759][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:51:04.762][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:04.764][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:04.767][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:51:04.767][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:51:04.767][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 01:51:04.767][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 01:51:04.767][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 01:51:04.770][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:51:04.774][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:04.776][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:04.779][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:51:04.781][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:04.786][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:04.788][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:51:04.790][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:04.793][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:51:04.796][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:51:04.799][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:04.801][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:04.804][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-17 01:51:04.810][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:04.813][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-17 01:51:04.816][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:04.822][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:51:04.825][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:04.827][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:51:04.830][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:04.834][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:51:04.836][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 01:51:04.839][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:51:04.843][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:04.846][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-17 01:51:04.849][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:51:04.851][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:04.856][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:04.860][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:04.862][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:51:04.865][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:04.869][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:04.873][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:51:04.875][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:04.877][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:04.880][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:51:04.882][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:04.885][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:51:04.888][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:51:04.891][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:04.893][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:04.896][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-17 01:51:04.900][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:04.906][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 01:51:04.909][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:04.912][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:51:04.916][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:04.919][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:51:04.922][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:04.924][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:51:04.927][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 01:51:04.930][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:51:04.933][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:04.936][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-17 01:51:04.939][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:51:04.941][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:04.944][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:04.947][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:04.949][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:51:04.951][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:04.953][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:04.956][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:51:04.958][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:04.962][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:04.964][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:51:04.967][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:04.969][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:51:04.972][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:51:04.976][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:04.978][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:04.982][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:51:04.985][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:04.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:04.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:04.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:04.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:04.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.002][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[2024-10-17 01:51:05.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.110][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[2024-10-17 01:51:05.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.220][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[2024-10-17 01:51:05.223][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-17 01:51:05.226][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-17 01:51:05.230][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-17 01:51:05.234][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-17 01:51:05.238][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 01:51:05.241][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-17 01:51:05.244][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-17 01:51:05.248][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-17 01:51:05.251][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-17 01:51:05.255][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-17 01:51:05.258][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 01:51:05.262][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-17 01:51:05.265][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-17 01:51:05.268][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-17 01:51:05.271][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-17 01:51:05.276][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 01:51:05.280][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-17 01:51:05.283][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-17 01:51:05.287][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 01:51:05.291][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-17 01:51:05.294][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-17 01:51:05.299][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-17 01:51:05.304][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-17 01:51:05.308][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-17 01:51:05.311][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-17 01:51:05.315][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-17 01:51:05.318][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-17 01:51:05.322][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-17 01:51:05.325][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-17 01:51:05.329][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-17 01:51:05.333][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-17 01:51:05.337][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-17 01:51:05.340][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-17 01:51:05.343][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-17 01:51:05.347][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-17 01:51:05.351][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-17 01:51:05.354][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-17 01:51:05.357][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-17 01:51:05.361][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-17 01:51:05.364][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-17 01:51:05.368][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-17 01:51:05.371][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-17 01:51:05.375][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-17 01:51:05.378][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-17 01:51:05.382][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-17 01:51:05.385][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-17 01:51:05.388][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-17 01:51:05.392][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-17 01:51:05.395][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-17 01:51:05.399][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-17 01:51:05.402][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-17 01:51:05.406][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-17 01:51:05.410][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-17 01:51:05.414][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-17 01:51:05.417][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-17 01:51:05.421][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-17 01:51:05.426][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-17 01:51:05.429][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-17 01:51:05.434][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-17 01:51:05.438][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-17 01:51:05.442][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-17 01:51:05.446][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-17 01:51:05.450][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-17 01:51:05.453][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-17 01:51:05.457][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-17 01:51:05.461][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-17 01:51:05.465][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 01:51:05.469][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 01:51:05.472][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-17 01:51:05.476][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-17 01:51:05.480][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-17 01:51:05.484][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-17 01:51:05.488][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-17 01:51:05.491][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-17 01:51:05.495][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-17 01:51:05.499][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-17 01:51:05.503][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-17 01:51:05.507][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-17 01:51:05.511][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-17 01:51:05.515][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-17 01:51:05.519][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-17 01:51:05.523][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-17 01:51:05.527][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-17 01:51:05.532][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-17 01:51:05.535][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-17 01:51:05.538][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:51:05.540][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.544][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:05.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:05.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:05.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:05.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:05.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:05.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:05.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:05.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:05.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:05.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:05.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:05.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:05.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:05.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:05.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:05.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:05.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:05.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.710][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[2024-10-17 01:51:05.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:05.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:05.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:05.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:05.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.743][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[2024-10-17 01:51:05.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:05.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:05.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.759][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[2024-10-17 01:51:05.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:05.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:05.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:05.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:05.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:05.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:05.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:05.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:05.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:05.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:05.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:05.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.846][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-10-17 01:51:05.851][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-10-17 01:51:05.856][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:05.858][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-17 01:51:05.861][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:05.864][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:51:05.866][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:05.868][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-10-17 01:51:05.871][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:05.873][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:51:05.876][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-17 01:51:05.878][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:51:05.882][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:05.886][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-10-17 01:51:05.888][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:51:05.891][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-10-17 01:51:05.891][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-10-17 01:51:05.891][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-10-17 01:51:05.891][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-10-17 01:51:05.891][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-10-17 01:51:05.891][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-10-17 01:51:05.891][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-10-17 01:51:05.891][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-10-17 01:51:05.891][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-10-17 01:51:05.891][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-10-17 01:51:05.891][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-10-17 01:51:05.891][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-10-17 01:51:05.891][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-10-17 01:51:05.891][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-10-17 01:51:05.891][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-10-17 01:51:05.891][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-10-17 01:51:05.891][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-10-17 01:51:05.891][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-10-17 01:51:05.894][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:05.896][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:51:05.896][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-10-17 01:51:05.896][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-10-17 01:51:05.899][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-17 01:51:05.902][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:05.904][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:05.906][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:51:05.909][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:05.912][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:05.916][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:51:05.919][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-10-17 01:51:05.919][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-10-17 01:51:05.922][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:51:05.924][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:51:05.927][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:05.930][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:05.933][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-10-17 01:51:05.937][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-17 01:51:05.942][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-17 01:51:05.946][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 01:51:05.950][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 01:51:05.959][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-10-17 01:51:05.961][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-10-17 01:51:05.964][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-10-17 01:51:05.968][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-17 01:51:05.971][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 01:51:05.973][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 01:51:05.976][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-10-17 01:51:05.979][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2024-10-17 01:51:05.981][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-10-17 01:51:05.981][self$setPropertyValue] Setting property "urls" to "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2024-10-17 01:51:05.984][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:51:05.987][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:51:05.989][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2024-10-17 01:51:06.000][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2024-10-17 01:51:06.002][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2024-10-17 01:51:06.006][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-17 01:51:06.009][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 01:51:06.013][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 01:51:06.016][private$addConnectorRules] Create new rule for URL "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-17 01:51:06.020][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 01:51:06.022][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2024-10-17 01:51:06.025][biodb::testThat]
biodb.INFO [2024-10-17 01:51:06.027][biodb::testThat] Running test function  test.hmdbmetabolite.nbentries  (" HMDB metabolite returns enough entries. ").
biodb.INFO [2024-10-17 01:51:06.030][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:51:06.032][biodb::testThat]
biodb.DEBUG[2024-10-17 01:51:06.053][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-17 01:51:06.057][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-17 01:51:06.061][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-10-17 01:51:06.065][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-17 01:51:06.067][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-10-17 01:51:06.070][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-10-17 01:51:06.073][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-10-17 01:51:06.075][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-10-17 01:51:06.078][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-10-17 01:51:06.085][conn$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2024-10-17 01:51:06.099][biodb::testThat]
biodb.INFO [2024-10-17 01:51:06.102][biodb::testThat] Running test function  test.old.accession  (" We can retrieve entries using old accession numbers. ").
biodb.INFO [2024-10-17 01:51:06.104][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:51:06.106][biodb::testThat]
biodb.DEBUG[2024-10-17 01:51:06.143][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2024-10-17 01:51:06.145][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-10-17 01:51:06.149][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-17 01:51:06.152][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-10-17 01:51:06.157][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2024-10-17 01:51:06.160][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:51:06.164][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2024-10-17 01:51:06.167][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:51:06.171][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:51:06.179][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-10-17 01:51:06.197][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:06.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:06.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:06.214][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:06.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:06.219][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:06.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:06.247][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:06.250][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:06.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.255][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:06.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:06.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.306][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:06.309][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:06.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.315][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.409][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:06.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:06.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.436][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 01:51:06.439][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 01:51:06.444][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.449][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.452][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 01:51:06.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 01:51:06.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.464][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 01:51:06.467][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 01:51:06.469][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.472][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.476][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 01:51:06.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 01:51:06.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.490][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:06.495][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:06.500][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.502][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:06.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:06.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.521][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:06.524][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:06.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.529][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:06.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:06.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.546][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:06.549][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:06.551][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.554][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.560][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:06.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:06.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.571][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:06.573][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:06.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.580][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.583][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:06.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:06.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.593][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:06.596][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:06.598][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.601][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.604][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:06.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:06.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.616][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:06.619][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:06.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.625][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.629][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:06.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:06.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.641][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:06.643][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:06.646][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.649][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.652][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:06.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:06.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.663][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:06.666][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:06.670][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.672][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.675][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:06.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:06.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.695][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:06.701][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:06.703][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.705][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.708][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:06.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:06.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.721][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:06.723][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:06.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.728][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:06.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:06.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.745][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:06.748][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:06.750][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.752][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.755][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:06.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:06.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.764][ef$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:06.766][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:06.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.771][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.774][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:06.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:06.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.783][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:06.787][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:06.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.794][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.797][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:06.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:06.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.808][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-10-17 01:51:06.812][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 01:51:06.815][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.818][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.821][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-10-17 01:51:06.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 01:51:06.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:06.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:06.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:06.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:06.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:06.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:06.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.975][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 01:51:06.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 01:51:06.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.988][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 01:51:06.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 01:51:06.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.999][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 01:51:07.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 01:51:07.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.010][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 01:51:07.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 01:51:07.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.020][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 01:51:07.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 01:51:07.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.030][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 01:51:07.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 01:51:07.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:07.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:07.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:07.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:07.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:07.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:07.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.068][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:07.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:07.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.078][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:07.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:07.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:07.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:07.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.098][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:07.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:07.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.108][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:07.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:07.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.117][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:07.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:07.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.128][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:07.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:07.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.137][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:07.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:07.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.147][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:07.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:07.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.158][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-17 01:51:07.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 01:51:07.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.167][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-17 01:51:07.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 01:51:07.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.178][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-17 01:51:07.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 01:51:07.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.189][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:07.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:07.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.200][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:07.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:07.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.210][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:07.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:07.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.227][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:07.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:07.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.238][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:07.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:07.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.248][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:07.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:07.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.259][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:07.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:07.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.269][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:07.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:07.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.279][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:07.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:07.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.289][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:07.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:07.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.298][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:07.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:07.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.308][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:07.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:07.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.316][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:07.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:07.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.324][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:07.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:07.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.334][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:07.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:07.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.344][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:07.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:07.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:07.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:07.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.365][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:07.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:07.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.375][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:07.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:07.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.385][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:07.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:07.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.395][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:07.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:07.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.405][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:07.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:07.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.415][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:07.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:07.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.425][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:07.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:07.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.436][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:07.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:07.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.447][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:07.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:07.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.457][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:07.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:07.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.467][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:07.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:07.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.477][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:07.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:07.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.488][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:07.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:07.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.498][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-10-17 01:51:07.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:07.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.509][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:07.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:07.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.519][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:07.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:07.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.529][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:07.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:07.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.540][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-10-17 01:51:07.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:07.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.611][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:07.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:07.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.623][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:07.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:07.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.634][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:07.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:07.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.644][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:07.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:07.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.653][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:07.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:07.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.663][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:51:07.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:51:07.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.673][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:51:07.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:51:07.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:07.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:07.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.695][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:51:07.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:51:07.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:07.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:07.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:07.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:07.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:07.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:07.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:07.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:07.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:07.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:07.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:07.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:07.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:07.772][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2024-10-17 01:51:07.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:07.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:07.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:07.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:07.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:07.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:07.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-17 01:51:07.821][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-17 01:51:07.824][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-10-17 01:51:07.827][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-10-17 01:51:07.829][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-17 01:51:07.831][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:07.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:07.837][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:07.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:07.842][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:07.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-17 01:51:07.855][biodb::testContext]
biodb.INFO [2024-10-17 01:51:07.858][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 01:51:07.861][biodb::testContext] Test context - Test search of entries
biodb.INFO [2024-10-17 01:51:07.863][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 01:51:07.865][biodb::testContext]
biodb.INFO [2024-10-17 01:51:07.878][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-17 01:51:07.893][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-17 01:51:07.900][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:51:07.905][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-17 01:51:07.908][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-17 01:51:07.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:07.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:07.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:07.917][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-17 01:51:07.922][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-17 01:51:07.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:07.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:07.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:07.934][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-17 01:51:07.937][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-17 01:51:07.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:07.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:07.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:07.945][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-17 01:51:07.948][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-17 01:51:07.950][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-17 01:51:07.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:07.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:07.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:07.960][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-17 01:51:07.963][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-17 01:51:07.965][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-17 01:51:07.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:07.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:07.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:07.984][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-17 01:51:07.987][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-17 01:51:07.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:07.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:07.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:07.997][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-17 01:51:08.000][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-17 01:51:08.003][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-17 01:51:08.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.010][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[2024-10-17 01:51:08.013][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-17 01:51:08.018][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-17 01:51:08.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.028][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-17 01:51:08.031][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-17 01:51:08.034][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-17 01:51:08.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.043][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-17 01:51:08.046][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-17 01:51:08.048][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-17 01:51:08.051][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-17 01:51:08.053][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-17 01:51:08.056][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-17 01:51:08.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.070][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-17 01:51:08.074][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-17 01:51:08.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.085][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-17 01:51:08.087][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-17 01:51:08.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.105][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-17 01:51:08.108][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-17 01:51:08.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.118][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[2024-10-17 01:51:08.120][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-17 01:51:08.124][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-17 01:51:08.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.136][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-17 01:51:08.139][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-17 01:51:08.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.149][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-17 01:51:08.152][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-17 01:51:08.175][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-17 01:51:08.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.185][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-17 01:51:08.187][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-17 01:51:08.190][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-17 01:51:08.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.198][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-17 01:51:08.203][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:08.205][self$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[2024-10-17 01:51:08.208][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:08.210][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:51:08.212][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:08.217][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:51:08.221][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:08.224][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:51:08.227][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 01:51:08.230][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:51:08.232][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:08.235][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-17 01:51:08.237][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:51:08.241][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:08.243][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:08.246][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:51:08.246][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:51:08.246][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 01:51:08.246][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 01:51:08.246][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 01:51:08.248][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:51:08.251][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:08.253][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:08.255][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:51:08.257][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:08.259][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:08.264][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:51:08.267][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:08.270][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:51:08.272][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:51:08.275][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:08.277][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:08.280][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-17 01:51:08.288][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:08.290][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 01:51:08.293][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:08.295][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:51:08.300][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:08.303][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:51:08.305][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:08.308][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:51:08.311][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 01:51:08.313][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:51:08.316][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:08.319][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-17 01:51:08.321][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:51:08.326][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:08.329][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:08.331][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:51:08.331][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:51:08.331][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 01:51:08.331][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 01:51:08.331][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 01:51:08.336][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:51:08.338][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:08.341][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:08.343][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:51:08.345][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:08.348][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:08.350][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:51:08.353][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:08.355][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:51:08.357][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:51:08.360][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:08.362][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:08.365][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-17 01:51:08.370][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:08.372][self$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[2024-10-17 01:51:08.375][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:08.377][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:51:08.379][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:08.382][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:51:08.384][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:08.387][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:51:08.389][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 01:51:08.392][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:51:08.394][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:08.405][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-17 01:51:08.409][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:51:08.412][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:08.414][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:08.417][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:08.420][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:51:08.423][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:08.425][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:08.427][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:51:08.430][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:08.432][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:08.434][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:51:08.437][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:08.439][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:51:08.442][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:51:08.445][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:08.447][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:08.450][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-17 01:51:08.455][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:08.457][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 01:51:08.460][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:08.463][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:51:08.466][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:08.469][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:51:08.471][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:08.478][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:51:08.481][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 01:51:08.483][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:51:08.486][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:08.490][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-17 01:51:08.493][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:51:08.495][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:08.498][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:08.503][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:08.506][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:51:08.508][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:08.511][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:08.515][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:51:08.518][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:08.520][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:08.523][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:51:08.526][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:08.528][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:51:08.531][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:51:08.533][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:08.535][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:08.540][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:51:08.543][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:08.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:08.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:08.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:08.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:08.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:08.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:08.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:08.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:08.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:08.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:08.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:08.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:08.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:08.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:08.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:08.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:08.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:08.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:08.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:08.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:08.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:08.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:08.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:08.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:08.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:08.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.766][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[2024-10-17 01:51:08.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:08.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:08.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.782][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[2024-10-17 01:51:08.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:08.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:08.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:08.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:08.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:08.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:08.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:08.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.827][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-17 01:51:08.836][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-17 01:51:08.839][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-17 01:51:08.845][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-17 01:51:08.849][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 01:51:08.852][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-17 01:51:08.857][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-17 01:51:08.870][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-17 01:51:08.874][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-17 01:51:08.879][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-17 01:51:08.883][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 01:51:08.887][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-17 01:51:08.891][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-17 01:51:08.894][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-17 01:51:08.899][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-17 01:51:08.903][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 01:51:08.906][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-17 01:51:08.913][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-17 01:51:08.918][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 01:51:08.922][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-17 01:51:08.926][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-17 01:51:08.929][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-17 01:51:08.934][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-17 01:51:08.940][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-17 01:51:08.945][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-17 01:51:08.950][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-17 01:51:08.954][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-17 01:51:08.958][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-17 01:51:08.964][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-17 01:51:08.968][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-17 01:51:08.971][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-17 01:51:08.975][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-17 01:51:08.979][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-17 01:51:08.982][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-17 01:51:08.989][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-17 01:51:08.992][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-17 01:51:08.996][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-17 01:51:09.000][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-17 01:51:09.003][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-17 01:51:09.007][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-17 01:51:09.011][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-17 01:51:09.015][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-17 01:51:09.019][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-17 01:51:09.022][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-17 01:51:09.026][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-17 01:51:09.030][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-17 01:51:09.033][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-17 01:51:09.037][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-17 01:51:09.040][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-17 01:51:09.045][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-17 01:51:09.049][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-17 01:51:09.053][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-17 01:51:09.056][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-17 01:51:09.060][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-17 01:51:09.063][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-17 01:51:09.066][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-17 01:51:09.069][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-17 01:51:09.072][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-17 01:51:09.074][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-17 01:51:09.077][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-17 01:51:09.080][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-17 01:51:09.084][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-17 01:51:09.090][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-17 01:51:09.094][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-17 01:51:09.097][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-17 01:51:09.101][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-17 01:51:09.104][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 01:51:09.109][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 01:51:09.112][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-17 01:51:09.116][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-17 01:51:09.120][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-17 01:51:09.123][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-17 01:51:09.129][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-17 01:51:09.133][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-17 01:51:09.140][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-17 01:51:09.143][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-17 01:51:09.149][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-17 01:51:09.153][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-17 01:51:09.158][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-17 01:51:09.162][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-17 01:51:09.165][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-17 01:51:09.169][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-17 01:51:09.173][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-17 01:51:09.178][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-17 01:51:09.182][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-17 01:51:09.184][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:51:09.187][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:09.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:09.192][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:09.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:09.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:09.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:09.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:09.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:09.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:09.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:09.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:09.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:09.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:09.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:09.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:09.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:09.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:09.225][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[2024-10-17 01:51:09.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:09.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:09.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:09.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:09.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:09.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:09.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:09.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:09.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:09.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:09.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:09.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:09.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:09.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:09.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:09.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:09.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:09.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:09.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:09.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:09.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:09.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:09.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:09.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:09.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:09.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:09.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:09.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:09.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:09.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:09.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:09.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:09.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:09.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:09.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:09.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:09.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:09.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:09.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:09.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:09.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:09.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:09.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:09.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:09.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:09.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:09.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:09.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:09.341][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[2024-10-17 01:51:09.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:09.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:09.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:09.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:09.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:09.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:09.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:09.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:09.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:09.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:09.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:09.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:09.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:09.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:09.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:09.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:09.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:09.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:09.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:09.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:09.384][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[2024-10-17 01:51:09.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:09.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:09.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:09.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:09.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:09.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:09.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:09.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:09.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:09.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:09.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:09.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:09.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:09.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:09.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:09.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:09.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:09.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:09.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:09.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:09.431][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[2024-10-17 01:51:09.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:09.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:09.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:09.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:09.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:09.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:09.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:09.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:51:09.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:09.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:09.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:09.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:09.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:09.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:09.484][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-10-17 01:51:09.488][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-10-17 01:51:09.492][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:09.498][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-17 01:51:09.501][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:09.503][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:51:09.513][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:09.515][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-10-17 01:51:09.518][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:09.521][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:51:09.524][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-17 01:51:09.526][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:51:09.529][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:09.531][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-10-17 01:51:09.538][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:51:09.542][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-10-17 01:51:09.542][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-10-17 01:51:09.542][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-10-17 01:51:09.542][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-10-17 01:51:09.542][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-10-17 01:51:09.542][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-10-17 01:51:09.542][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-10-17 01:51:09.542][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-10-17 01:51:09.542][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-10-17 01:51:09.542][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-10-17 01:51:09.542][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-10-17 01:51:09.542][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-10-17 01:51:09.542][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-10-17 01:51:09.542][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-10-17 01:51:09.542][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-10-17 01:51:09.542][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-10-17 01:51:09.542][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-10-17 01:51:09.542][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-10-17 01:51:09.547][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-17 01:51:09.550][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:51:09.550][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-10-17 01:51:09.550][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-10-17 01:51:09.552][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-17 01:51:09.555][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:09.557][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:09.559][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:51:09.562][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:51:09.564][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:51:09.567][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:51:09.569][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-10-17 01:51:09.569][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-10-17 01:51:09.572][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:51:09.576][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:51:09.578][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-17 01:51:09.580][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:51:09.586][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-10-17 01:51:09.590][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-17 01:51:09.594][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-17 01:51:09.598][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 01:51:09.602][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 01:51:09.611][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-10-17 01:51:09.613][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-10-17 01:51:09.617][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-10-17 01:51:09.622][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-17 01:51:09.624][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 01:51:09.627][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 01:51:09.639][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-10-17 01:51:09.642][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.DEBUG[2024-10-17 01:51:09.644][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-10-17 01:51:09.644][self$setPropertyValue] Setting property "urls" to "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip".
biodb.DEBUG[2024-10-17 01:51:09.646][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:51:09.649][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:51:09.652][FUN] Trying to call function notifyConnUrlsUpdated on observer BiodbRequestScheduler.
biodb.DEBUG[2024-10-17 01:51:09.655][FUN] Functions in observer BiodbRequestScheduler: [15]: ".__enclos_env__, clone, getAllRules, unregisterConnector, registerConnector, getConnectorRules, findRule, getUrl, getUrlString, notifyConnSchedulerFrequencyUpdated, notifyConnUrlsUpdated, downloadFile, sendRequest, sendSoapRequest, initialize".
biodb.DEBUG[2024-10-17 01:51:09.658][self$registerConnector] Register connector hmdb.metabolites.
biodb.DEBUG[2024-10-17 01:51:09.661][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-17 01:51:09.664][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 01:51:09.666][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 01:51:09.669][private$addConnectorRules] Create new rule for URL "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbHmdb/extdata/generated/hmdb_extract.zip" of connector "hmdb.metabolites".
biodb.DEBUG[2024-10-17 01:51:09.672][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 01:51:09.676][self$setFrequency] t=1.000000, n=3.000000
biodb.INFO [2024-10-17 01:51:09.680][biodb::testThat]
biodb.INFO [2024-10-17 01:51:09.683][biodb::testThat] Running test function  test.searchMultipleWordsInDescription  (" We can search for multiple words inside description field. ").
biodb.INFO [2024-10-17 01:51:09.685][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:51:09.688][biodb::testThat]
biodb.DEBUG[2024-10-17 01:51:09.692][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2024-10-17 01:51:09.695][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2024-10-17 01:51:09.698][private$doSearchForEntries] fields VALUES = and
biodb.DEBUG[2024-10-17 01:51:09.706][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-17 01:51:09.709][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-17 01:51:09.713][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-10-17 01:51:09.716][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-17 01:51:09.719][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-10-17 01:51:09.722][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-10-17 01:51:09.725][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-10-17 01:51:09.727][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-10-17 01:51:09.730][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-10-17 01:51:09.732][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-10-17 01:51:09.734][private$doSearchForEntries] Total number of IDs = 2
biodb.DEBUG[2024-10-17 01:51:09.740][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-10-17 01:51:09.742][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-10-17 01:51:09.747][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-17 01:51:09.751][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-10-17 01:51:09.756][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2024-10-17 01:51:09.759][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:51:09.763][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2024-10-17 01:51:09.767][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:51:09.770][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:51:09.773][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-10-17 01:51:09.777][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:09.779][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:09.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:09.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:09.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:09.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:09.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:09.807][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:09.810][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:09.813][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.816][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:09.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:09.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.831][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:09.834][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:09.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.839][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.842][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:09.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:09.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.852][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 01:51:09.855][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 01:51:09.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.861][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.864][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 01:51:09.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 01:51:09.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.875][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 01:51:09.879][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 01:51:09.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.884][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.887][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 01:51:09.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 01:51:09.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.898][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:09.901][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:09.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.906][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.910][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:09.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:09.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.921][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:09.924][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:09.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.928][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.932][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:09.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:09.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.943][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:09.946][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:09.948][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.950][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.956][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:09.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:09.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.967][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:09.969][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:09.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.974][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.978][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:09.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:09.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.992][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:09.994][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:09.997][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.000][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.003][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:10.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:10.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.014][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:10.017][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:10.029][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.031][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.037][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:10.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:10.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.049][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:10.052][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:10.055][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.059][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.062][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:10.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:10.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.077][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:10.080][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:10.082][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.089][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.094][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:10.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:10.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.112][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:10.115][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:10.120][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.122][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.125][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:10.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:10.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.139][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:10.144][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:10.147][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.150][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:10.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:10.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.170][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:10.177][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:10.179][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.181][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.184][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:10.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:10.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.196][ef$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:10.203][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:10.206][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.209][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.212][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:10.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:10.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.223][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:10.233][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:10.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.238][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.241][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:10.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:10.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.256][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-10-17 01:51:10.259][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 01:51:10.263][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.265][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.269][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-10-17 01:51:10.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 01:51:10.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:10.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:10.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:10.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:10.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:10.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:10.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.314][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 01:51:10.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 01:51:10.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.324][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 01:51:10.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 01:51:10.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.346][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 01:51:10.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 01:51:10.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.362][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 01:51:10.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 01:51:10.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.376][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 01:51:10.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 01:51:10.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.388][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 01:51:10.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 01:51:10.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.402][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:10.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:10.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:10.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:10.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:10.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:10.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.436][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:10.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:10.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:10.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:10.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:10.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:10.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.477][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:10.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:10.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.491][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:10.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:10.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.515][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:10.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:10.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.527][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:10.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:10.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.541][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:10.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:10.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.554][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:10.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:10.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.565][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-17 01:51:10.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 01:51:10.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.578][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-17 01:51:10.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 01:51:10.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.592][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-17 01:51:10.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 01:51:10.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.605][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:10.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:10.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.619][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:10.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:10.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.631][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:10.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:10.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.642][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:10.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:10.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.654][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:10.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:10.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.667][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:10.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:10.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.681][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:10.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:10.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.703][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:10.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:10.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.718][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:10.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:10.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.731][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:10.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:10.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.745][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:10.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:10.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.757][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:10.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:10.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.770][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:10.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:10.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.781][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:10.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:10.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.796][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:10.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:10.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:10.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:10.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:10.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:10.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.834][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:10.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:10.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.845][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:10.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:10.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.858][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:10.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:10.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.873][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:10.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:10.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.885][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:10.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:10.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.896][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:10.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:10.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.909][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:10.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:10.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.920][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:10.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:10.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.932][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:10.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:10.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.941][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:10.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:10.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.964][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:10.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:10.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.974][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:10.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:10.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.988][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:10.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:10.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.999][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-10-17 01:51:11.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:11.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.011][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:11.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:11.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.025][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:11.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:11.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.035][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:11.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:11.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.047][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-10-17 01:51:11.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:11.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.060][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:11.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:11.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.073][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:11.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:11.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.086][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:11.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:11.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.103][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:11.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:11.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.117][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:11.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:11.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.131][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:51:11.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:51:11.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.145][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:51:11.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:51:11.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:11.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:11.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.170][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:51:11.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:51:11.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:11.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:11.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:11.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:11.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:11.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:11.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:11.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:11.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:11.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:11.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:11.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:11.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:11.260][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2024-10-17 01:51:11.264][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:11.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:11.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.276][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:11.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:11.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.291][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:11.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:11.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.303][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:11.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:11.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:11.315][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-10-17 01:51:11.318][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-10-17 01:51:11.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:11.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:11.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:11.343][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:11.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:11.348][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:11.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:11.413][private$loadEntries] Creating entries from ids [1]: "HMDB0000002".
biodb.DEBUG[2024-10-17 01:51:11.570][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-10-17 01:51:11.577][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-17 01:51:11.580][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-10-17 01:51:11.635][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000002".
biodb.TRACE[2024-10-17 01:51:11.639][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:51:11.642][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml".
biodb.DEBUG[2024-10-17 01:51:11.646][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:51:11.728][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:51:11.732][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-10-17 01:51:11.736][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:11.742][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:11.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:11.761][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:11.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:11.768][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:11.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:11.790][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:11.793][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:11.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.798][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:11.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:11.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.818][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:11.820][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:11.823][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.827][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.831][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:11.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:11.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.846][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 01:51:11.849][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 01:51:11.852][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.854][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.858][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 01:51:11.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 01:51:11.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.871][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 01:51:11.875][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 01:51:11.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.880][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.883][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 01:51:11.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 01:51:11.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.897][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:11.900][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:11.903][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.906][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:11.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:11.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.925][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:11.928][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:11.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.933][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.937][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:11.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:11.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.948][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:11.951][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:11.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.956][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.962][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:11.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:11.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.976][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:11.980][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:11.982][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.988][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.991][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:11.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:11.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.003][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:12.005][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:12.008][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.011][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.013][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:12.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:12.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.025][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:12.027][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:12.030][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.036][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.039][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:12.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:12.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.052][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:12.055][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:12.060][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.064][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.066][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:12.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:12.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.077][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:12.080][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:12.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.088][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.091][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:12.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:12.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.104][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:12.107][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:12.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.113][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.116][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:12.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:12.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.130][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:12.132][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:12.137][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.139][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.142][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:12.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:12.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.156][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:12.161][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:12.163][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.167][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.171][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:12.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:12.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.188][ef$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:12.192][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:12.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.196][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.202][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:12.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:12.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.214][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:12.217][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:12.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.231][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.234][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:12.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:12.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.246][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-10-17 01:51:12.251][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 01:51:12.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.256][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.258][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-10-17 01:51:12.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 01:51:12.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:12.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:12.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:12.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:12.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:12.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:12.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.320][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 01:51:12.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 01:51:12.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.335][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 01:51:12.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 01:51:12.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.348][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 01:51:12.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 01:51:12.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.359][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 01:51:12.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 01:51:12.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.370][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 01:51:12.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 01:51:12.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.384][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-10-17 01:51:12.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-10-17 01:51:12.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:12.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:12.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.411][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:12.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:12.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:12.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:12.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.435][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:12.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:12.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:12.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:12.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.459][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:12.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-10-17 01:51:12.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.472][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:12.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:12.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.486][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:12.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:12.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.499][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:12.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-10-17 01:51:12.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.512][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:12.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:12.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.523][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:12.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:12.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.535][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:12.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-10-17 01:51:12.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.550][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-17 01:51:12.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 01:51:12.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.562][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-17 01:51:12.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 01:51:12.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.572][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-10-17 01:51:12.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-10-17 01:51:12.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.584][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:12.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:12.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.599][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:12.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:12.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.611][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:12.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:12.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.627][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:12.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:12.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.637][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:12.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:12.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.650][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:12.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:12.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.664][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:12.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:12.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.708][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:12.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:12.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.719][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:12.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:12.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.729][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:12.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:12.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.740][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:12.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:12.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.753][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:12.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:12.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.766][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:12.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:12.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.778][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:12.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:12.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.788][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:12.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:12.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.801][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:12.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:12.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.814][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:12.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:12.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.827][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:12.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:12.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.839][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:12.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:12.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.851][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:12.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:12.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.865][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:12.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:12.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.876][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:12.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:12.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.888][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:12.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:12.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.900][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:12.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-10-17 01:51:12.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.911][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:12.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:12.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.921][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:12.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:12.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.933][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:12.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-10-17 01:51:12.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.946][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:12.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:12.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.957][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:12.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:12.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.969][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:12.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:12.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.980][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-10-17 01:51:12.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:12.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.991][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:12.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:12.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.003][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:13.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:13.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.014][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:13.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:13.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.024][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-10-17 01:51:13.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:13.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.037][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:13.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:13.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.048][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:13.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:13.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.058][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:13.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:13.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.069][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:13.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:13.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.080][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:13.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:13.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.091][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:51:13.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:51:13.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.109][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:51:13.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:51:13.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:13.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:13.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.131][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:51:13.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-10-17 01:51:13.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:13.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:13.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:13.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:13.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:13.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:13.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:13.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:13.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:13.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:13.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:13.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:13.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:13.224][self$createEntryFromContent] Accession numbers: HMDB0000002.
biodb.TRACE[2024-10-17 01:51:13.253][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:13.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:13.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.278][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:13.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:13.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.292][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:13.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:13.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.307][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:13.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:13.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:13.322][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-10-17 01:51:13.325][private$doSearchForEntries] COUNT IDS = 2
biodb.DEBUG[2024-10-17 01:51:13.328][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:13.330][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:13.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:13.349][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:13.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:13.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:13.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:13.614][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2024-10-17 01:51:13.617][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2024-10-17 01:51:13.619][private$doSearchForEntries] fields VALUES = c("histidine", "cerebrovascular")
biodb.DEBUG[2024-10-17 01:51:13.666][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-17 01:51:13.672][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-17 01:51:13.676][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-10-17 01:51:13.684][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-17 01:51:13.686][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-10-17 01:51:13.752][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-10-17 01:51:13.755][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-10-17 01:51:13.758][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-10-17 01:51:13.761][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-10-17 01:51:13.764][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-10-17 01:51:13.768][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-10-17 01:51:13.773][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:13.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:13.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.784][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:13.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:13.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.795][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:13.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:13.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.807][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:13.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:13.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.820][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:13.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:13.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.831][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:13.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:13.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.853][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:13.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:13.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:13.865][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-10-17 01:51:13.867][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-10-17 01:51:13.872][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:13.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:13.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:13.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:13.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:13.899][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:13.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:13.903][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:13.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:13.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.916][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:13.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:13.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.929][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:13.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:13.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.942][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:13.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:13.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.954][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:13.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:13.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.967][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:13.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:13.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.980][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:13.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:13.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:13.995][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2024-10-17 01:51:13.999][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-10-17 01:51:14.003][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:14.005][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:14.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:14.022][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:14.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:14.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:14.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:14.054][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2024-10-17 01:51:14.057][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2024-10-17 01:51:14.061][private$doSearchForEntries] fields VALUES = c("monoalkylamines", "shiitakes")
biodb.DEBUG[2024-10-17 01:51:14.067][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-17 01:51:14.071][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-17 01:51:14.077][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-10-17 01:51:14.080][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-10-17 01:51:14.083][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-10-17 01:51:14.089][private$doListFiles] List files in /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-10-17 01:51:14.091][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-10-17 01:51:14.094][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-10-17 01:51:14.099][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-10-17 01:51:14.103][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-10-17 01:51:14.106][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-10-17 01:51:14.113][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:14.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:14.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.125][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:14.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:14.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.138][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:14.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:14.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.150][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:14.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:14.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.161][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:14.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:14.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.172][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:14.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:14.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.182][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:14.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:14.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:14.194][private$doSearchForEntries] MATCHED = FALSE
biodb.DEBUG[2024-10-17 01:51:14.197][private$doSearchForEntries] COUNT IDS = 0
biodb.DEBUG[2024-10-17 01:51:14.200][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:14.203][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:14.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:14.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:14.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:14.224][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:14.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:14.233][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:14.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:14.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.247][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:14.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:14.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.259][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:14.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:14.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.270][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:14.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:14.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.283][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:14.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:14.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.294][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:14.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:14.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.306][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-10-17 01:51:14.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-10-17 01:51:14.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:14.319][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-10-17 01:51:14.321][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-10-17 01:51:14.326][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:14.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:14.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:14.344][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:14.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:14.354][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:14.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-17 01:51:14.377][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-17 01:51:14.380][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-10-17 01:51:14.383][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-10-17 01:51:14.387][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-17 01:51:14.392][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:14.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:14.397][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:14.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:14.406][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:14.408][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 85 ]
> 
> proc.time()
   user  system elapsed 
 14.778   0.778  18.587

Example timings

biodbHmdb.Rcheck/biodbHmdb-Ex.timings

name	user	system	elapsed
HmdbMetabolitesConn	3.962	1.176	6.302
HmdbMetabolitesEntry	0.743	0.032	0.996
hmdbToSqlite	4.643	0.097	7.371